Alignments for a candidate for gdhA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Desulfovibrio vulgaris Hildenborough

Align Probable NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2 (characterized)
to candidate 206396 DVU0964 Glu/Leu/Phe/Val dehydrogenase family protein

Query= SwissProt::Q9USN5
         (1106 letters)



>MicrobesOnline__882:206396
          Length = 997

 Score =  289 bits (740), Expect = 6e-82
 Identities = 201/569 (35%), Positives = 297/569 (52%), Gaps = 55/569 (9%)

Query: 538  NEEDVSVMEMFVKFNTHLLKTNFFQTTKVALSFRFDPSFLDST---QYKDPLYAMIMSIG 594
            +E + +V+ M  +F    L+TN+F      LSFR DP FL +    + ++  Y +    G
Sbjct: 391  DESERTVLLMVHRFFAFTLRTNYFLEDVYGLSFRLDPQFLPAPCRIEGEELPYGIFFFHG 450

Query: 595  NEFRGFHLRFRDVARGGIRLIKSANPEAFGLNARGLFDENYNLAKTQMLKNKDIPEGGAK 654
                GFH+R+RD++RGG+R++ + + E F L +  L+DE   LA  Q +KNKDIPEGG+K
Sbjct: 451  PYCMGFHIRYRDMSRGGVRVVPTRSAEQFELESNRLYDEVKGLAYAQQVKNKDIPEGGSK 510

Query: 655  GVILLGKDCQDKPELAFMKYIDSIIDLLIVNKSQP----LVDKLGKPEILFMGPDEN-TA 709
             VILLG     +  +A M   +S++D+++  +S P    +VD LGK EI+++GPDEN T 
Sbjct: 511  AVILLGPLGDIRLAVASMG--NSLLDVILCGESSPTLPGVVDHLGKEEIIYLGPDENITP 568

Query: 710  DLVNWATIHAHRRNAPWWKSFFTGKKPTMGGIPHDKYGMTSLSVRCYVEGIYKKLNITDP 769
            + + W    A +R   W  +F + K     GI H +YG+TSL V  + E + + L I   
Sbjct: 569  EHITWIVERARQRGYRWPSAFMSSKPGA--GINHKQYGVTSLGVMVFAEEVLRHLGIDPA 626

Query: 770  SKLTKVQ-TGGPDGDLGSNEIKL------SNEKYIAVIDGSGVLYDPAGLDRTELLRLAD 822
            ++   V+ TGGP GD+  N +++       N + +AV DG G  YDP GLDR EL+RL D
Sbjct: 627  AQPFTVKITGGPKGDVAGNLMRIMFRDYGDNARVVAVTDGHGAAYDPEGLDRAELMRLVD 686

Query: 823  ERKTIDHFDAGKLSPEGYRVLVKDTNLKLPNGEIVRNGTIFRNTAHLRYKADTFVPCGGR 882
             +++ID FDA  L  EG  V+         + E VR     RN  H   +AD F+P GGR
Sbjct: 687  GQRSIDSFDAALLRGEGAFVV------SARDPETVR----LRNALHNTARADIFIPSGGR 736

Query: 883  PNAININNVEQLIDDHGRPAFKYLVEGANLFITQDAKSVLEKAGVIVIRDASANKGGVTS 942
            PN IN+ N  +  D  G P  + +VEGANLF++ DA+  L + GV+V+  +SANK GV  
Sbjct: 737  PNTINMRNWHEFFDGDGVPTARAIVEGANLFVSPDARKRLAERGVLVVHGSSANKTGVIC 796

Query: 943  SSLEVLASLSFDDASF---KENMCVHDGKVPTFYADYVNEVKRIIQRNANLEFEAIWK-- 997
            SS EVL  L   D  F   KE               YV +V  I++R A  E   +    
Sbjct: 797  SSYEVLGGLVMTDGEFIAAKER--------------YVADVFDILRRRARDEARLLLAEL 842

Query: 998  GHSENKIPYTSLSNHLSTEIVKLDHDIYN-YEKLWADVG----FRNAVLRASIPKTLQAK 1052
               +   P   +S   S E+      +Y  + +   D+     +R  VL    P  L  K
Sbjct: 843  RRCDRCKPLHVISVEASQEMNHAADALYGAFMQRQLDIAEDSLWRGLVL-DYCPAVLVEK 901

Query: 1053 IGLEKMLERIPESYLRAIFSTYLASRFVY 1081
               +++ + +P  +L A+ + Y AS  VY
Sbjct: 902  F-RDRIFDMVPRRHLYALIAAYAASAIVY 929


Lambda     K      H
   0.319    0.135    0.393 

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: 2073
Number of extensions: 101
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: 1106
Length of database: 997
Length adjustment: 45
Effective length of query: 1061
Effective length of database: 952
Effective search space:  1010072
Effective search space used:  1010072
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: 58 (26.9 bits)

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

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Protein sequences (fasta format)
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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