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.5720.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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.73
//
[ok]

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

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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:

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:

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:

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:

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