Alignments for a candidate for prpB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Shewanella amazonensis SB2B

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate 6939200 Sama_3294 2-methylisocitrate lyase (RefSeq)

Query= SwissProt::Q8EJW1
         (292 letters)



>FitnessBrowser__SB2B:6939200
          Length = 294

 Score =  508 bits (1309), Expect = e-149
 Identities = 259/292 (88%), Positives = 274/292 (93%)

Query: 1   MTQSAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGM 60
           MT SAG RFR ALA SKPLQIVGTTNAYFALMAE+TGFQALYLSGAGVANASYGLPDLGM
Sbjct: 1   MTHSAGKRFRDALARSKPLQIVGTTNAYFALMAEKTGFQALYLSGAGVANASYGLPDLGM 60

Query: 61  TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKR 120
           TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEK+GVAAVHMEDQVSQKR
Sbjct: 61  TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKVGVAAVHMEDQVSQKR 120

Query: 121 CGHRPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGA 180
           CGHRPNKAVVSTEEMVDRIKAAVDARTD NFVIMARTDAVAVEGL+AGIERA+AYI AGA
Sbjct: 121 CGHRPNKAVVSTEEMVDRIKAAVDARTDENFVIMARTDAVAVEGLDAGIERAQAYIEAGA 180

Query: 181 DMIFAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRA 240
           DMIFAEALTEL QYR FK  VKAPILANMTEFGQT+LF+K  L +AGADMVLYPLGTFRA
Sbjct: 181 DMIFAEALTELPQYRKFKDAVKAPILANMTEFGQTELFDKSALYEAGADMVLYPLGTFRA 240

Query: 241 ANQAALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292
           ANQAALKVMQALMNDGHQRNVL TMQ+R +LY++L YH+FED LD+LF++ K
Sbjct: 241 ANQAALKVMQALMNDGHQRNVLSTMQSRKELYEFLNYHSFEDTLDRLFAEGK 292


Lambda     K      H
   0.319    0.132    0.369 

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: 408
Number of extensions: 10
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: 292
Length of database: 294
Length adjustment: 26
Effective length of query: 266
Effective length of database: 268
Effective search space:    71288
Effective search space used:    71288
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: 48 (23.1 bits)

Align candidate 6939200 Sama_3294 (2-methylisocitrate lyase (RefSeq))
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

# 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/TIGR02317.hmm
# target sequence database:        /tmp/gapView.2402.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02317  [M=285]
Accession:   TIGR02317
Description: prpB: methylisocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.7e-132  424.7   2.9   8.8e-132  424.5   2.9    1.0  1  lcl|FitnessBrowser__SB2B:6939200  Sama_3294 2-methylisocitrate lya


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939200  Sama_3294 2-methylisocitrate lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.5   2.9  8.8e-132  8.8e-132       2     284 ..       6     289 ..       5     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 424.5 bits;  conditional E-value: 8.8e-132
                         TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtklpll 77 
                                       gk++r++l+++++lqi+G+ na+ al+aek+Gf+a+YlsGa++a+ s glPDlg+t++++v+ +a rit++t+lpll
  lcl|FitnessBrowser__SB2B:6939200   6 GKRFRDALARSKPLQIVGTTNAYFALMAEKTGFQALYLSGAGVANaSYGLPDLGMTSMNDVLIDAGRITSATQLPLL 82 
                                       799*****************************************989****************************** PP

                         TIGR02317  78 vDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvliaRtDa 154
                                       vD+DtG+G+a+n+art+ke+e+ gvaavh+eDqv +k+CGh+++k++vs+eemv++ikaav+a++de+fv++aRtDa
  lcl|FitnessBrowser__SB2B:6939200  83 VDIDTGWGGAFNIARTIKEFEKVGVAAVHMEDQVSQKRCGHRPNKAVVSTEEMVDRIKAAVDARTDENFVIMARTDA 159
                                       ***************************************************************************** PP

                         TIGR02317 155 raveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleelgykiviyPvt 231
                                        aveGlda ieRa+aY+eaGad+if+eal+++ ++r+f++avk+p+lanmtefG+t l+  + l e+g ++v+yP+ 
  lcl|FitnessBrowser__SB2B:6939200 160 VAVEGLDAGIERAQAYIEAGADMIFAEALTELPQYRKFKDAVKAPILANMTEFGQTELFDKSALYEAGADMVLYPLG 236
                                       ***************************************************************************** PP

                         TIGR02317 232 alRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                       ++Raa++aa kv++ l+++G q+++l ++q RkelYe l+y+++e+++++lf+
  lcl|FitnessBrowser__SB2B:6939200 237 TFRAANQAALKVMQALMNDGHQRNVLSTMQSRKELYEFLNYHSFEDTLDRLFA 289
                                       ************************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (294 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.30
//
[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