Alignments for a candidate for prpE in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Dechlorosoma suillum PS

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate Dsui_2925 Dsui_2925 propionate--CoA ligase

Query= BRENDA::P77495
         (628 letters)



>FitnessBrowser__PS:Dsui_2925
          Length = 630

 Score =  817 bits (2110), Expect = 0.0
 Identities = 390/627 (62%), Positives = 493/627 (78%), Gaps = 3/627 (0%)

Query: 2   SFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRW 61
           S+ EF++RSI +P+ FW+EQA+ IDW  PF Q  D+S PPFA+WF  G+TNLC+NA+DR 
Sbjct: 3   SYKEFHRRSIEQPDAFWSEQAQLIDWHKPFDQVCDYSRPPFAKWFVGGQTNLCYNAVDRH 62

Query: 62  LEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEA 121
            + +P   ALI +S+ET+ E+ ++F +L  EV  +A++ +SLGV++GDRVL+YMPMIAEA
Sbjct: 63  AKTRPNDNALIFISTETDVEKVYSFAELQREVERMAAIYQSLGVKKGDRVLIYMPMIAEA 122

Query: 122 HITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDDA 181
              +LACARIGAIHSVVFGGFAS S+A RIDDAKPVLIVS+DAG RGGK +PYK LLDDA
Sbjct: 123 CFAILACARIGAIHSVVFGGFASGSLATRIDDAKPVLIVSSDAGMRGGKAVPYKHLLDDA 182

Query: 182 ISQAQHQPRHVLLVDRGLAK-MARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240
           I+QA+H+P  VL+VDRGL K   +V GRDVD+A+LR Q + A+VPV W+ES++ S ILYT
Sbjct: 183 INQAEHKPGKVLMVDRGLDKAFNKVEGRDVDYAALRAQFMDAQVPVTWVESSDPSYILYT 242

Query: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300
           SGTTGKPKGVQRD GGYAVALA+S+  I+ GK G  FF  SDIGWVVGHSYI+Y PL+ G
Sbjct: 243 SGTTGKPKGVQRDTGGYAVALASSIKHIYCGKPGETFFSTSDIGWVVGHSYIIYGPLIGG 302

Query: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360
           MATI+YEG P  PD G+WW IVEKY+V+ MFSAPTA RVLKK   A + K+DLSSL+ L+
Sbjct: 303 MATIMYEGTPIRPDAGIWWQIVEKYKVNVMFSAPTAARVLKKHDPAFLHKYDLSSLKHLF 362

Query: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420
           LAGEPLD+PT  W+   L +PVIDNYWQTE+GWP+++  RG++D   + G+P  P+YGY+
Sbjct: 363 LAGEPLDQPTHEWIMGELKLPVIDNYWQTETGWPMLSTVRGVEDTKIKYGTPSFPVYGYD 422

Query: 421 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRP-VYATFDW 479
           V++  E  G  C  NEKG+L V  PLPPGC+ T+WGDD RFV TY+SLF  P VY+++DW
Sbjct: 423 VRIFRE-DGSECDANEKGILGVVPPLPPGCLTTVWGDDERFVNTYFSLFKEPLVYSSYDW 481

Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539
            I+D +GYHFILGRTDDVINVAGHRLGTREIEE++  HP VAEVAVVGV DALKGQ+ VA
Sbjct: 482 AIKDDEGYHFILGRTDDVINVAGHRLGTREIEEAVQGHPAVAEVAVVGVNDALKGQLPVA 541

Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599
           F + K++  +   ++  + EK +M  VD  +G   RP  V+F+S LPKTRSGK+LRR+IQ
Sbjct: 542 FAVVKDASKIATPELVAALEKEVMKRVDETLGAIARPGRVYFISGLPKTRSGKLLRRSIQ 601

Query: 600 AICEGRDPGDLTTIDDPASLDQIRQAM 626
           A+ EGRDPGDLTTI+DP +L+QI+ A+
Sbjct: 602 ALAEGRDPGDLTTIEDPTALEQIKAAL 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: 1210
Number of extensions: 45
Number of successful extensions: 4
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: 630
Length adjustment: 38
Effective length of query: 590
Effective length of database: 592
Effective search space:   349280
Effective search space used:   349280
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 Dsui_2925 Dsui_2925 (propionate--CoA ligase)
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.1729.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 1086.6   0.1          0 1086.4   0.1    1.0  1  lcl|FitnessBrowser__PS:Dsui_2925  Dsui_2925 propionate--CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2925  Dsui_2925 propionate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1086.4   0.1         0         0       2     627 ..       3     629 ..       2     630 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1086.4 bits;  conditional E-value: 0
                         TIGR02316   2 ayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlalvavsset 78 
                                       +y+e+++rsie+p+afw+eqa+ idw+ pf +v d+s++pfa+wfvgg+tnlcynavdrh ++r+++ al+ +s+et
  lcl|FitnessBrowser__PS:Dsui_2925   3 SYKEFHRRSIEQPDAFWSEQAQLIDWHKPFDQVCDYSRPPFAKWFVGGQTNLCYNAVDRHAKTRPNDNALIFISTET 79 
                                       7**************************************************************************** PP

                         TIGR02316  79 geertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfggfashslaariddat 155
                                       + e+ +++ +l rev+++a++ ++lgv++gdrvliy+pmiaea +a+lacarigaihsvvfggfas sla+ridda+
  lcl|FitnessBrowser__PS:Dsui_2925  80 DVEKVYSFAELQREVERMAAIYQSLGVKKGDRVLIYMPMIAEACFAILACARIGAIHSVVFGGFASGSLATRIDDAK 156
                                       ***************************************************************************** PP

                         TIGR02316 156 pklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglak.lrrvpgrdvdyaalrrqhedadvevewles 231
                                       p+livs+dag+rggk ++yk+lld+ai++a hkp +vl+vdrgl+k +++v grdvdyaalr q +da+v+v w+es
  lcl|FitnessBrowser__PS:Dsui_2925 157 PVLIVSSDAGMRGGKAVPYKHLLDDAINQAEHKPGKVLMVDRGLDKaFNKVEGRDVDYAALRAQFMDAQVPVTWVES 233
                                       **********************************************99***************************** PP

                         TIGR02316 232 nepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfsasdvgwvvghsyivyapllaglatvlyeg 308
                                       ++psyilytsgttgkpkgvqrd+ggyavala s++ i+ +k g+++fs+sd+gwvvghsyi+y+pl+ g+at++yeg
  lcl|FitnessBrowser__PS:Dsui_2925 234 SDPSYILYTSGTTGKPKGVQRDTGGYAVALASSIKHIYCGKPGETFFSTSDIGWVVGHSYIIYGPLIGGMATIMYEG 310
                                       ***************************************************************************** PP

                         TIGR02316 309 lptrpdggvwwsivekyrvsvmfsaptairvlkkqdaallrkhdlsslevlflagepldeptarwisdalgkpvidn 385
                                       +p+rpd+g+ww+iveky+v+vmfsapta rvlkk+d+a l+k+dlssl++lflagepld+pt +wi   l  pvidn
  lcl|FitnessBrowser__PS:Dsui_2925 311 TPIRPDAGIWWQIVEKYKVNVMFSAPTAARVLKKHDPAFLHKYDLSSLKHLFLAGEPLDQPTHEWIMGELKLPVIDN 387
                                       ***************************************************************************** PP

                         TIGR02316 386 ywqtetgwpvlaiarglddkpvklgspglpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarfl 462
                                       ywqtetgwp+l+ +rg++d   k+g+p +pvygy+++++ e  g ++ +nekg+l v++plppgcl+tvwgdd rf+
  lcl|FitnessBrowser__PS:Dsui_2925 388 YWQTETGWPMLSTVRGVEDTKIKYGTPSFPVYGYDVRIFRE-DGSECDANEKGILGVVPPLPPGCLTTVWGDDERFV 463
                                       ***************************************99.699******************************** PP

                         TIGR02316 463 ktyfsafkrl.lyssldwgirdedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvav 538
                                       +tyfs+fk++ +yss+dw+i+d++gy+filgrtddvinvaghrlgtreiee+v  h+avaevavvgv+d+lkgq++v
  lcl|FitnessBrowser__PS:Dsui_2925 464 NTYFSLFKEPlVYSSYDWAIKDDEGYHFILGRTDDVINVAGHRLGTREIEEAVQGHPAVAEVAVVGVNDALKGQLPV 540
                                       ********7537***************************************************************** PP

                         TIGR02316 539 afailkeadsvedaddahalekelmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdlttidd 615
                                       afa++k+a++++ ++   aleke+m+ v++ lga+arp rvy+++ lpktrsgkllrr+iqa+aegrdpgdltti+d
  lcl|FitnessBrowser__PS:Dsui_2925 541 AFAVVKDASKIATPELVAALEKEVMKRVDETLGAIARPGRVYFISGLPKTRSGKLLRRSIQALAEGRDPGDLTTIED 617
                                       ***************************************************************************** PP

                         TIGR02316 616 paaleqvreale 627
                                       p+aleq++ al 
  lcl|FitnessBrowser__PS:Dsui_2925 618 PTALEQIKAALS 629
                                       ********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (630 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: 8.66
//
[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:

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