Alignments for a candidate for prpB in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Halomonas desiderata SP1

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate WP_086511658.1 BZY95_RS20055 methylisocitrate lyase

Query= SwissProt::Q8EJW1
         (292 letters)



>NCBI__GCF_002151265.1:WP_086511658.1
          Length = 301

 Score =  386 bits (991), Expect = e-112
 Identities = 196/293 (66%), Positives = 233/293 (79%), Gaps = 1/293 (0%)

Query: 1   MTQ-SAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLG 59
           MTQ + G RFR AL  ++PL IVGT NAY A+MAE+ G QA+YLSG GVANAS+GLPDLG
Sbjct: 1   MTQPTPGARFRAALEANRPLPIVGTINAYTAMMAERVGHQAIYLSGGGVANASFGLPDLG 60

Query: 60  MTSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQK 119
           MTSMNDV+ DA RI  AT LPLLVDIDTGWGGAFNIART+KE ++ GVAAVH+EDQV+QK
Sbjct: 61  MTSMNDVVQDAHRICGATDLPLLVDIDTGWGGAFNIARTVKEMQRAGVAAVHLEDQVAQK 120

Query: 120 RCGHRPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAG 179
           RCGHRPNK +VS +EMVDRIKAA DAR DP+F ++ARTDA   EGL+A IERA A I AG
Sbjct: 121 RCGHRPNKEIVSKQEMVDRIKAAADARIDPDFYLIARTDAFQKEGLDAAIERANACIEAG 180

Query: 180 ADMIFAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFR 239
           AD IFAEA+  LD YR F  +V APILAN+TEFG T LF ++EL + G  MVLYPL  FR
Sbjct: 181 ADAIFAEAVHTLDDYRAFCERVDAPILANITEFGATPLFTQQELGEVGCRMVLYPLSAFR 240

Query: 240 AANQAALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292
           A N AALKV +++   GHQR+V++ MQTR +LY +L YHAFE KLD LF++++
Sbjct: 241 AMNAAALKVYRSIHEKGHQRDVVELMQTRDELYDFLNYHAFEQKLDALFAENQ 293


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: 298
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: 301
Length adjustment: 26
Effective length of query: 266
Effective length of database: 275
Effective search space:    73150
Effective search space used:    73150
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 WP_086511658.1 BZY95_RS20055 (methylisocitrate lyase)
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.18977.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-131  423.1   0.9   2.8e-131  422.9   0.9    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511658.1  BZY95_RS20055 methylisocitrate l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511658.1  BZY95_RS20055 methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.9   0.9  2.8e-131  2.8e-131       2     284 ..       7     290 ..       6     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 422.9 bits;  conditional E-value: 2.8e-131
                                 TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearrit 69 
                                               g+++r++l+++ +l i+G+ina++a++ae++G++a+YlsG+++a+ s+glPDlg+t++++v+++a+ri 
  lcl|NCBI__GCF_002151265.1:WP_086511658.1   7 GARFRAALEANRPLPIVGTINAYTAMMAERVGHQAIYLSGGGVANaSFGLPDLGMTSMNDVVQDAHRIC 75 
                                               689*****************************************989********************** PP

                                 TIGR02317  70 rvtklpllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaav 138
                                                +t+lpllvD+DtG+G+a+n+artvke+++agvaavh+eDqva+k+CGh+++ke+vsk+emv++ikaa+
  lcl|NCBI__GCF_002151265.1:WP_086511658.1  76 GATDLPLLVDIDTGWGGAFNIARTVKEMQRAGVAAVHLEDQVAQKRCGHRPNKEIVSKQEMVDRIKAAA 144
                                               ********************************************************************* PP

                                 TIGR02317 139 kakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtef 207
                                               +a+ d+df+liaRtDa   eGldaaieRa+a +eaGadaif+ea+++++++r f+++v++p+lan+tef
  lcl|NCBI__GCF_002151265.1:WP_086511658.1 145 DARIDPDFYLIARTDAFQKEGLDAAIERANACIEAGADAIFAEAVHTLDDYRAFCERVDAPILANITEF 213
                                               ********************************************************************* PP

                                 TIGR02317 208 GktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedye 276
                                               G tpl+t +el e+g ++v+yP++a+Ra++ aa kvy+++++kG q+++++ +qtR+elY+ l+y+++e
  lcl|NCBI__GCF_002151265.1:WP_086511658.1 214 GATPLFTQQELGEVGCRMVLYPLSAFRAMNAAALKVYRSIHEKGHQRDVVELMQTRDELYDFLNYHAFE 282
                                               ********************************************************************* PP

                                 TIGR02317 277 kkdkelfk 284
                                               +k++ lf+
  lcl|NCBI__GCF_002151265.1:WP_086511658.1 283 QKLDALFA 290
                                               ***99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (301 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: 00:00:00.00
# Mc/sec: 11.46
//
[ok]

This GapMind analysis is from Sep 24 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