Alignments for a candidate for gcvP in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Sphingomonas histidinilytica UM2

Align Probable glycine dehydrogenase (decarboxylating) subunit 2; EC 1.4.4.2; Glycine cleavage system P-protein subunit 2; Glycine decarboxylase subunit 2; Glycine dehydrogenase (aminomethyl-transferring) subunit 2 (uncharacterized)
to candidate WP_079648577.1 B5X82_RS12945 glycine dehydrogenase subunit 2

Query= curated2:Q9A354
         (524 letters)



>NCBI__GCF_900167915.1:WP_079648577.1
          Length = 524

 Score =  688 bits (1776), Expect = 0.0
 Identities = 358/527 (67%), Positives = 404/527 (76%), Gaps = 8/527 (1%)

Query: 1   MNNVGRPTRPEAANDAANGHETLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDL 60
           MN+ GR TRPE    AA    T TG R L+ +E LIFE D + +TGVDLP      +  L
Sbjct: 3   MNSEGRVTRPETTVAAAQAPATFTGNRALMLEEGLIFERDDYARTGVDLPEAPRV-AGRL 61

Query: 61  NGLLRDAPIGLPGLSEPETVRHYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARLPG 120
            GL R  PIGLPGL+EPE VRHY RLS++N+AIDL L+PLGSCTMKHNPRLNEKMARLPG
Sbjct: 62  GGLERSRPIGLPGLTEPEAVRHYTRLSRQNYAIDLGLFPLGSCTMKHNPRLNEKMARLPG 121

Query: 121 FSDIHPLQPQSTVQGALELMDRLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAHEA 180
           F+DIHPL P  TVQGAL ++D LA WL TLTGM AVA++PKAGAHGELCGLLAIRAAH+A
Sbjct: 122 FADIHPLAPVDTVQGALAVIDELAQWLITLTGMHAVAMSPKAGAHGELCGLLAIRAAHDA 181

Query: 181 AGNGHRKTVLAPTSAHGTNPATAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIMVT 240
           AG+  R  +L P SAHGTNPATAAF GY V  I  T DGRVDLA L ++LG  VA +M+T
Sbjct: 182 AGSD-RSVILVPESAHGTNPATAAFCGYKVENIPATADGRVDLAALTARLGPDVAGVMIT 240

Query: 241 NPNTCGLFERDVVEIARLTHAAGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTFST 300
           NPNTCGLFERD+  I+   HAAG Y YCDGANFNAIVGRVRPGDLG+DAMHINLHKTFST
Sbjct: 241 NPNTCGLFERDMKRISDAVHAAGGYVYCDGANFNAIVGRVRPGDLGIDAMHINLHKTFST 300

Query: 301 PHGGGGPGAGPVVLSEALAPFAPTPWLT-HGDNGFELA-EHAGDDDAKTAFGRMSAFHGQ 358
           PHGGGGPG+GPVVLSEALAP+AP P++    D  F+L  E    +D   +FGRM+AFHGQ
Sbjct: 301 PHGGGGPGSGPVVLSEALAPYAPLPFVARQADGSFKLVEEETAGEDHPGSFGRMTAFHGQ 360

Query: 359 MGMYVRAYAYMLSHGADGLRQVAEDAVLNANYIKAQLKDVMSPAFPE-GPCMHEALFDDS 417
           MGM+ RA  Y+LSHGADGLRQV+EDAVLNANY+   L D++   F + GPCMHEALF D 
Sbjct: 361 MGMFTRALTYILSHGADGLRQVSEDAVLNANYVLRSLDDLLDAPFGDSGPCMHEALFSDE 420

Query: 418 WLEGTGVTTLDFAKAMIDEGFHPMTMYFPLVVHGAMLIEPTETESKHELDRFIAALRALA 477
            L   G TTLD AK +IDEGFHPMTMYFPLVVHGAMLIEPTETESK  LD+FI ALR++A
Sbjct: 421 GL-AQGFTTLDIAKGLIDEGFHPMTMYFPLVVHGAMLIEPTETESKAALDQFIGALRSVA 479

Query: 478 GAAKAGDTERFKGAPFHAPLRRLDETQAARKPRLRWKPVAAAPLAAE 524
             A+AGD E  K AP  AP RRLDET AARKP L WK   A P AAE
Sbjct: 480 SRARAGD-EALKAAPALAPRRRLDETAAARKPVLVWKD-DALPQAAE 524


Lambda     K      H
   0.318    0.135    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: 956
Number of extensions: 41
Number of successful extensions: 7
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: 524
Length of database: 524
Length adjustment: 35
Effective length of query: 489
Effective length of database: 489
Effective search space:   239121
Effective search space used:   239121
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 24 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 2024 update 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