Alignments for a candidate for prpB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Shewanella loihica PV-4

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate 5209346 Shew_1820 2-methylisocitrate lyase (RefSeq)

Query= SwissProt::Q8EJW1
         (292 letters)



>FitnessBrowser__PV4:5209346
          Length = 292

 Score =  417 bits (1073), Expect = e-121
 Identities = 209/289 (72%), Positives = 241/289 (83%)

Query: 4   SAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGMTSM 63
           SAG +FRQALA++KPLQIVGT NAY A+MA+Q G +A+YLSG GVANASYGLPDLGMTS+
Sbjct: 2   SAGKKFRQALADNKPLQIVGTINAYTAMMAKQIGHKAIYLSGGGVANASYGLPDLGMTSL 61

Query: 64  NDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKRCGH 123
           NDV++D  RITSA  LPLLVDIDTGWGGAFNIA+TIK+ EK G AAVHMEDQV+QKRCGH
Sbjct: 62  NDVIVDVQRITSACDLPLLVDIDTGWGGAFNIAKTIKDMEKAGAAAVHMEDQVAQKRCGH 121

Query: 124 RPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGADMI 183
           RPNK +VS EEMVDRIKAAVDARTDP+F IMARTDA A EGLEA IERAKAY+AAGAD I
Sbjct: 122 RPNKEIVSVEEMVDRIKAAVDARTDPDFFIMARTDAFAQEGLEAAIERAKAYVAAGADGI 181

Query: 184 FAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRAANQ 243
           FAEA+   + YR F   +  PILAN+TEFGQT+L+N+E+L Q GA MVLYPL  FRA N+
Sbjct: 182 FAEAVKTEEHYRAFAEALDVPILANITEFGQTELWNREQLGQWGAAMVLYPLSAFRAMNK 241

Query: 244 AALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292
           AA  V Q ++ DG Q+ VLDTMQTR +LY YLGYHA+E KLD LF++ K
Sbjct: 242 AAENVYQTILRDGDQKAVLDTMQTRMELYDYLGYHAYEQKLDSLFAEGK 290


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: 297
Number of extensions: 7
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: 292
Length adjustment: 26
Effective length of query: 266
Effective length of database: 266
Effective search space:    70756
Effective search space used:    70756
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 5209346 Shew_1820 (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.6944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   8.8e-133  427.8   3.7     1e-132  427.6   3.7    1.0  1  lcl|FitnessBrowser__PV4:5209346  Shew_1820 2-methylisocitrate lya


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209346  Shew_1820 2-methylisocitrate lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.6   3.7    1e-132    1e-132       2     284 ..       4     287 ..       3     288 .. 0.99

  Alignments for each domain:
  == domain 1  score: 427.6 bits;  conditional E-value: 1e-132
                        TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtklpllv 78 
                                      gk++r++l+ +++lqi+G+ina++a++a++ G++a+YlsG+++a+ s glPDlg+t+l++v+ +++rit++++lpllv
  lcl|FitnessBrowser__PV4:5209346   4 GKKFRQALADNKPLQIVGTINAYTAMMAKQIGHKAIYLSGGGVANaSYGLPDLGMTSLNDVIVDVQRITSACDLPLLV 81 
                                      799*****************************************989******************************* PP

                        TIGR02317  79 DaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvliaRtDara 156
                                      D+DtG+G+a+n+a+t+k++e+ag+aavh+eDqva+k+CGh+++ke+vs eemv++ikaav+a++d+df+++aRtDa a
  lcl|FitnessBrowser__PV4:5209346  82 DIDTGWGGAFNIAKTIKDMEKAGAAAVHMEDQVAQKRCGHRPNKEIVSVEEMVDRIKAAVDARTDPDFFIMARTDAFA 159
                                      ****************************************************************************** PP

                        TIGR02317 157 veGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleelgykiviyPvtalR 234
                                      +eGl+aaieRakaYv aGad if+ea+++ee++r fa+a++vp+lan+tefG+t l++ ++l + g ++v+yP++a+R
  lcl|FitnessBrowser__PV4:5209346 160 QEGLEAAIERAKAYVAAGADGIFAEAVKTEEHYRAFAEALDVPILANITEFGQTELWNREQLGQWGAAMVLYPLSAFR 237
                                      ****************************************************************************** PP

                        TIGR02317 235 aalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                      a++kaae+vy+++ ++G qk++ld++qtR elY+ lgy++ye+k+++lf+
  lcl|FitnessBrowser__PV4:5209346 238 AMNKAAENVYQTILRDGDQKAVLDTMQTRMELYDYLGYHAYEQKLDSLFA 287
                                      **********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (292 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.96
//
[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