GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Bacteroides clarus YIT 12056

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_009123247.1 BUB52_RS02020 NADP-specific glutamate dehydrogenase

Query= BRENDA::Q9TVN3
         (438 letters)



>NCBI__GCF_900129655.1:WP_009123247.1
          Length = 445

 Score =  595 bits (1535), Expect = e-175
 Identities = 285/438 (65%), Positives = 352/438 (80%), Gaps = 2/438 (0%)

Query: 1   MKDLEARNPAQPEFIQASREVIESIIDVVNSNPKYLENKILERITEPNLIHEFKVEWEND 60
           M  LEA++P + E++QA +EV+ SI D+ N +P++ + KI+ER+ EP+ I  F+V W +D
Sbjct: 7   MSSLEAKHPGESEYLQAVKEVLLSIEDIYNQHPEFEKAKIIERLVEPDRIFTFRVTWVDD 66

Query: 61  KHEIMVNKGYRIQFNNAIGPYKGGLRFHRAVTLGTLKFLGFEQIFKNSLTGLPMGGGKGG 120
           K E+  N GYR+QFNNAIGPYKGG+RFH +V L  LKFLGFEQ FKN+LT LPMGGGKGG
Sbjct: 67  KGEVQTNLGYRVQFNNAIGPYKGGIRFHASVNLSILKFLGFEQTFKNALTTLPMGGGKGG 126

Query: 121 SDFDPRGKSDAEILRFCRSFMTSLFKYIGPEIDVPAGDIGVGGREIGYLFGQYKRLTQQH 180
           SDF PRGKSDAE++RFC++FM  L++++GP++DVPAGDIGVGGRE+GY+FG YK+LT++ 
Sbjct: 127 SDFSPRGKSDAEVMRFCQAFMLELWRHLGPDMDVPAGDIGVGGREVGYMFGMYKKLTREF 186

Query: 181 EGVLTGKGLNWGGSLVRPEATGFGTMYFANEVLHAHGDDIKGKTIAISGFGNVAFGAVLK 240
            G  TGKGL +GGSL+RPEATGFG +YF +++L   G DIKGKT+AISGFGNVA+GA  K
Sbjct: 187 TGTFTGKGLEFGGSLIRPEATGFGGLYFVHQMLETKGIDIKGKTVAISGFGNVAWGAATK 246

Query: 241 AKQLGAKVVTISGPDGYIYDENGINTDEKINYMLELRASNNDVVAPFAEKF-GAKFIPGK 299
           A QLGAKV+TISGPDGYIYD NGI + EKI+YMLELRAS ND+VAP+A++F G+ F+PGK
Sbjct: 247 ATQLGAKVITISGPDGYIYDPNGI-SGEKIDYMLELRASGNDIVAPYADEFPGSTFVPGK 305

Query: 300 KPWEVPVDMAFPCAIQNELNAEDAATLHKNGVKYVIETSNMGCTADAVQYFIKNRIVFAP 359
           +PWEV  D+A PCA QNELN EDA  L  N V  V E SNMGCT +A+  FI+N+I++AP
Sbjct: 306 RPWEVKADIALPCATQNELNGEDAQHLIDNKVTCVGEISNMGCTPEAIDLFIENKIMYAP 365

Query: 360 GKAANAGGVAVSGLEMSQNSMKLNWTAEEVDAKLKNIMTNIHASCVKEGKESDGYINYVK 419
           GKA NAGGVA SGLEMSQN+M ++W+A EVD KL  IM  IH  CVK G E DGYINYVK
Sbjct: 366 GKAVNAGGVATSGLEMSQNAMHISWSAAEVDEKLHAIMHGIHTQCVKYGTEPDGYINYVK 425

Query: 420 GANIAGFKKVADAMVDLG 437
           GANIAGF KVA AM+  G
Sbjct: 426 GANIAGFMKVAHAMMGQG 443


Lambda     K      H
   0.317    0.137    0.405 

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: 679
Number of extensions: 30
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: 438
Length of database: 445
Length adjustment: 32
Effective length of query: 406
Effective length of database: 413
Effective search space:   167678
Effective search space used:   167678
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

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:

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:

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:

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:

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