Alignments for a candidate for prpE in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Herbaspirillum seropedicae SmR1

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate HSERO_RS15645 HSERO_RS15645 acetyl-CoA synthetase

Query= BRENDA::P77495
         (628 letters)



>FitnessBrowser__HerbieS:HSERO_RS15645
          Length = 628

 Score =  923 bits (2385), Expect = 0.0
 Identities = 434/628 (69%), Positives = 533/628 (84%)

Query: 1   MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60
           M + +FY++S+ +PE FWA++A+RI WQ PF++TLD+S PPFARWF +G+TNLCHNA+DR
Sbjct: 1   MQYEQFYRQSVEQPEAFWAQEAQRIHWQQPFSRTLDYSRPPFARWFIDGQTNLCHNAVDR 60

Query: 61  WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120
            L ++ +  ALIA+S+ET  ER +T+ +L  EV A+A+ +++LGVQRGDRVL+YMPMIAE
Sbjct: 61  HLPERAQQAALIAISTETNSERVYTYAELQQEVMAMAASMQALGVQRGDRVLIYMPMIAE 120

Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180
           A   +LACARIGA+HSVVFGGFAS+S+A+RIDDA+P LIVSADAG+RGGK+IPYK LLD+
Sbjct: 121 AVFAMLACARIGAVHSVVFGGFASNSLASRIDDAQPRLIVSADAGSRGGKVIPYKGLLDE 180

Query: 181 AISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240
           AI+ AQH+P+HVLLVDRGLA MAR + RDVD+A LR QH+G +VPV WLESN +S ILYT
Sbjct: 181 AIAMAQHRPQHVLLVDRGLAPMARTAQRDVDYAPLRTQHLGQQVPVTWLESNASSYILYT 240

Query: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300
           SGTTGKPKGVQRDVGGYAVALA+SM  IF G+ G  +FC SDIGWVVGHSYIVY PL+AG
Sbjct: 241 SGTTGKPKGVQRDVGGYAVALASSMQHIFCGQPGETYFCTSDIGWVVGHSYIVYGPLIAG 300

Query: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360
           MAT++YEGLP  PD G+WW+IVEKY+V+RMFSAPTAIRVLKK P   + ++D SSL+ LY
Sbjct: 301 MATVLYEGLPIRPDAGIWWSIVEKYKVTRMFSAPTAIRVLKKQPPECMERYDTSSLKALY 360

Query: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420
           LAGEPLDE T+SW+S  L VPVIDNYWQTESGWPI++IA+G+DD+PTRLGSPGVPM GY 
Sbjct: 361 LAGEPLDETTSSWISGALKVPVIDNYWQTESGWPIISIAKGIDDKPTRLGSPGVPMPGYR 420

Query: 421 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDWG 480
           + +L+E TGEPCG ++KG++ +EGPLPPGC+QT++GDD RFV TYW    R VY+TFDWG
Sbjct: 421 LAILDEATGEPCGPDQKGVVAIEGPLPPGCMQTVYGDDERFVNTYWRSLPREVYSTFDWG 480

Query: 481 IRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAF 540
           IRD DGY+FILGRTDDVINVAGHRLGTREIEESISSHP V+EVAVVGV+D LKGQVA AF
Sbjct: 481 IRDKDGYYFILGRTDDVINVAGHRLGTREIEESISSHPNVSEVAVVGVEDKLKGQVAFAF 540

Query: 541 VIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQA 600
            IPK++ ++   +   + E  IMA+VD QIG  GRPA V+FVS LPKTRSGK+LRR IQ+
Sbjct: 541 AIPKQAYTIATPEQRKALEAEIMAVVDKQIGAVGRPARVFFVSGLPKTRSGKLLRRAIQS 600

Query: 601 ICEGRDPGDLTTIDDPASLDQIRQAMEE 628
           ICEGRDPGDL TI+DPA+L+Q+R  +++
Sbjct: 601 ICEGRDPGDLPTIEDPAALEQVRAVIKD 628


Lambda     K      H
   0.320    0.136    0.422 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1227
Number of extensions: 37
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 628
Length of database: 628
Length adjustment: 38
Effective length of query: 590
Effective length of database: 590
Effective search space:   348100
Effective search space used:   348100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate HSERO_RS15645 HSERO_RS15645 (acetyl-CoA synthetase)
to HMM TIGR02316 (prpE: propionate--CoA ligase (EC 6.2.1.17))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02316.hmm
# target sequence database:        /tmp/gapView.13121.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02316  [M=628]
Accession:   TIGR02316
Description: propion_prpE: propionate--CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                  Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
          0 1150.8   0.1          0 1150.7   0.1    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS15645  HSERO_RS15645 acetyl-CoA synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS15645  HSERO_RS15645 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1150.7   0.1         0         0       1     626 [.       1     626 [.       1     628 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1150.7 bits;  conditional E-value: 0
                                  TIGR02316   1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeq 68 
                                                m+ye++y++s+e+peafwa++a+ri+wq pf+r+ld+s++pfarwf++g+tnlc+navdrhl +r++q
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645   1 MQYEQFYRQSVEQPEAFWAQEAQRIHWQQPFSRTLDYSRPPFARWFIDGQTNLCHNAVDRHLPERAQQ 68 
                                                78****************************************************************** PP

                                  TIGR02316  69 lalvavssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihs 136
                                                +al+a+s+et+ er +ty +l +ev a+a+ ++algv+rgdrvliy+pmiaea++a+lacariga+hs
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645  69 AALIAISTETNSERVYTYAELQQEVMAMAASMQALGVQRGDRVLIYMPMIAEAVFAMLACARIGAVHS 136
                                                ******************************************************************** PP

                                  TIGR02316 137 vvfggfashslaariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglaklrr 204
                                                vvfggfas+sla ridda+p+livsadag+rggkvi+yk lld+aia aqh+p+hvllvdrgla+++r
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645 137 VVFGGFASNSLASRIDDAQPRLIVSADAGSRGGKVIPYKGLLDEAIAMAQHRPQHVLLVDRGLAPMAR 204
                                                ******************************************************************** PP

                                  TIGR02316 205 vpgrdvdyaalrrqhedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgak 272
                                                ++ rdvdya lr+qh + +v+v wlesn +syilytsgttgkpkgvqrdvggyavala sm+ if ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645 205 TAQRDVDYAPLRTQHLGQQVPVTWLESNASSYILYTSGTTGKPKGVQRDVGGYAVALASSMQHIFCGQ 272
                                                ******************************************************************** PP

                                  TIGR02316 273 agdvlfsasdvgwvvghsyivyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvl 340
                                                 g+++f++sd+gwvvghsyivy+pl+ag+atvlyeglp+rpd+g+wwsiveky+v++mfsaptairvl
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645 273 PGETYFCTSDIGWVVGHSYIVYGPLIAGMATVLYEGLPIRPDAGIWWSIVEKYKVTRMFSAPTAIRVL 340
                                                ******************************************************************** PP

                                  TIGR02316 341 kkqdaallrkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvk 408
                                                kkq++  + ++d ssl+ l+lageplde t++wis al +pvidnywqte+gwp+++ia+g+ddkp++
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645 341 KKQPPECMERYDTSSLKALYLAGEPLDETTSSWISGALKVPVIDNYWQTESGWPIISIAKGIDDKPTR 408
                                                ******************************************************************** PP

                                  TIGR02316 409 lgspglpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarflktyfsafkrllyss 476
                                                lgspg+p++gyrl +ldeatge++gp++kg++++++plppgc++tv+gdd rf++ty+  ++r +ys+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645 409 LGSPGVPMPGYRLAILDEATGEPCGPDQKGVVAIEGPLPPGCMQTVYGDDERFVNTYWRSLPREVYST 476
                                                ******************************************************************** PP

                                  TIGR02316 477 ldwgirdedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvavafailk 544
                                                +dwgird+dgy filgrtddvinvaghrlgtreiees+ssh++v+evavvgv+d+lkgqva afai+k
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645 477 FDWGIRDKDGYYFILGRTDDVINVAGHRLGTREIEESISSHPNVSEVAVVGVEDKLKGQVAFAFAIPK 544
                                                ******************************************************************** PP

                                  TIGR02316 545 eadsvedaddahalekelmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdltt 612
                                                +a +++ +++++ale+e+ma+v++q+gav+rparv++v+ lpktrsgkllrraiq+++egrdpgdl t
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645 545 QAYTIATPEQRKALEAEIMAVVDKQIGAVGRPARVFFVSGLPKTRSGKLLRRAIQSICEGRDPGDLPT 612
                                                ******************************************************************** PP

                                  TIGR02316 613 iddpaaleqvreal 626
                                                i+dpaaleqvr  +
  lcl|FitnessBrowser__HerbieS:HSERO_RS15645 613 IEDPAALEQVRAVI 626
                                                ***********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (628 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 9.25
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources