Alignments for a candidate for iolA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolA in Pseudomonas stutzeri RCH2

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF3712 Psest_3781 methylmalonic acid semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__psRCH2:GFF3712
          Length = 500

 Score =  607 bits (1564), Expect = e-178
 Identities = 302/499 (60%), Positives = 375/499 (75%), Gaps = 4/499 (0%)

Query: 1   MTLIKHLIGGELIADTG-RTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNT 59
           M  + +LI  E +A    R A V+NP+ GE    V L+  +  ++AI AA+AAF  W  T
Sbjct: 1   MQTLGNLINNEAVAGRSERHATVYNPANGEPRLYVSLSSADETREAIAAAQAAFDGWSKT 60

Query: 60  PPAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILK 119
           PP  RA+V+FRFK+LLE   + + +LI+ EHGK   DA GE+ RG+E VE+A   P +LK
Sbjct: 61  PPLVRARVMFRFKELLERRRDDVARLITSEHGKVFSDAQGEVTRGLEVVEFACGIPHLLK 120

Query: 120 GEYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPS 179
           GE+S NVG +ID+ S  QP+GV  GITPFNFPAMVPLWM P+AIACGNTF+LKPSE+DPS
Sbjct: 121 GEFSSNVGRDIDSNSLMQPLGVCVGITPFNFPAMVPLWMLPVAIACGNTFVLKPSEKDPS 180

Query: 180 STLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKR 239
           +T+L+ EL  EAGLP GVLN+V+GDK AVD L+    V+++SFVGSTPIAEYIY+  +  
Sbjct: 181 ATMLLGELLAEAGLPAGVLNIVNGDKEAVDVLLTDERVQSVSFVGSTPIAEYIYATASAH 240

Query: 240 GKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQ 299
           GKR QALGGAKNH V+MPDAD    VS+L+GAAYGS GERCMAISVAVCVGD++AD LV 
Sbjct: 241 GKRCQALGGAKNHMVVMPDADPQQVVSSLIGAAYGSAGERCMAISVAVCVGDEVADKLVG 300

Query: 300 KLVPQIKGLKIGAGTSCGLD--MGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAG 357
            L  +I  ++ G G     +  MGPLVT   + KV+GYID GV +GA LV DGRG KV G
Sbjct: 301 MLQDEIGQMRTGPGLGIEPEPHMGPLVTREHQQKVSGYIDLGVEEGATLVCDGRGIKVEG 360

Query: 358 HENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTR 417
           HENGF++G TLFDRVTP M IY+EEIFGPVL +VRV S +EA+QLINDHEYGNGT IFTR
Sbjct: 361 HENGFYVGPTLFDRVTPSMRIYREEIFGPVLAVVRVKSFDEALQLINDHEYGNGTSIFTR 420

Query: 418 DGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAI 477
           DG+ AR F + ++VGMVGVNVP+PVP+A+H FGGWKRS+FG L+ +GPDGVRF+T+ K +
Sbjct: 421 DGDTARQFEENVKVGMVGVNVPIPVPMAFHCFGGWKRSVFGPLNMHGPDGVRFFTRMKTV 480

Query: 478 TQRWPQRKSHEAAQFAFPS 496
           T+RWP       A+FA P+
Sbjct: 481 TRRWP-TGIRAGAEFAMPT 498


Lambda     K      H
   0.319    0.137    0.411 

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: 747
Number of extensions: 28
Number of successful extensions: 3
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: 498
Length of database: 500
Length adjustment: 34
Effective length of query: 464
Effective length of database: 466
Effective search space:   216224
Effective search space used:   216224
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 (21.7 bits)
S2: 52 (24.6 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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