GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Desulfobacter vibrioformis DSM 8776

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_000745975.1:WP_035241269.1
          Length = 485

 Score =  317 bits (813), Expect = 4e-91
 Identities = 177/472 (37%), Positives = 273/472 (57%), Gaps = 6/472 (1%)

Query: 14  FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73
           FI  +++ +   K     NPAT E LGTV   GA E   A+ AA  +L   W+  TA +R
Sbjct: 15  FIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPA-WRSKTAAQR 73

Query: 74  IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133
            A+LR+  DL++E +E+L++L + + GKP   S   +I  AA  F +F++  + I  +  
Sbjct: 74  SAILRRWHDLLMENQEDLALLMTAEQGKPLAESRG-EIAYAASFFEWFAEEAKRIYGDII 132

Query: 134 QMDDVALNYA-IRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
                +     I++PVGV+  I PWN P  ++T K   ALAAG T+V+KPA  TP +A  
Sbjct: 133 PQTIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPATATPFSALA 192

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
           +A++ ++AG+P GV N+V G   ++ G  LT +P V  ++FTG T  GK +M   A T+K
Sbjct: 193 IAKLAQEAGMPPGVFNVVTG-SSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDCAGTMK 251

Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312
           R+S ELGG  P ++F D++LD  +E  +   + N G+ C+C +R+YV+   Y+ F EK  
Sbjct: 252 RVSMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQFCEKLA 311

Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFL 372
                L VG+  +     G LI  +  E V  +I  A+++G  +L GGKR      G F 
Sbjct: 312 RAVATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKR--HALGGTFF 369

Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432
            PT++  +T D  V KEEIFGP   +  F++E EV+++ NDT YGL+A  +T D+ R  R
Sbjct: 370 SPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDMARTWR 429

Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
           V  ++E G++ +N+  + +   PFGG+K+SG GREG  +  + Y E+  +C+
Sbjct: 430 VGEKLEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481


Lambda     K      H
   0.318    0.136    0.404 

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: 594
Number of extensions: 27
Number of successful extensions: 5
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: 486
Length of database: 485
Length adjustment: 34
Effective length of query: 452
Effective length of database: 451
Effective search space:   203852
Effective search space used:   203852
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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