GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Desulfobacter vibrioformis DSM 8776

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>NCBI__GCF_000745975.1:WP_035241269.1
          Length = 485

 Score =  285 bits (728), Expect = 3e-81
 Identities = 168/462 (36%), Positives = 255/462 (55%), Gaps = 13/462 (2%)

Query: 23  SSPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDD 82
           ++P    V+  V   G  E   A+ AA  +L  AW   + AQR  +L    D +    +D
Sbjct: 32  TNPATGEVLGTVPFCGADETRRAIDAANGSLP-AWRSKTAAQRSAILRRWHDLLMENQED 90

Query: 83  FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAV-R 141
                  + GKP++ +R  +I   A+ F+ FA+  K +  +      P  + +    V +
Sbjct: 91  LALLMTAEQGKPLAESRG-EIAYAASFFEWFAEEAKRIYGDII----PQTIASQRLVVIK 145

Query: 142 RPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPG 201
           +PVGVV  I PWN P  ++T K G ALA G T+VVKP+  TP +A  + ++   AG+PPG
Sbjct: 146 QPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPATATPFSALAIAKLAQEAGMPPG 205

Query: 202 VYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAI 261
           V+NVV G      GE LT++P V  +TFTG T  G+ +M+  A   + VS+ELGG    I
Sbjct: 206 VFNVVTGSSSAIGGE-LTANPIVRKLTFTGSTEVGKKLMQDCAGTMKRVSMELGGNAPFI 264

Query: 262 VFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPED 321
           VF D DLD A+EG L   + N GQ C+   R+YV+  ++D+F  +L +    +++G   +
Sbjct: 265 VFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQFCEKLARAVATLKVGNGIE 324

Query: 322 LATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGD 381
                GPLI  +  E V  +   A++ GA V+ GG    +     GG +  PT+   + D
Sbjct: 325 EGVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKRHAL-----GGTFFSPTVLADVTD 379

Query: 382 DSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIA 441
           D +VA+EEIFGP A +  F+SE EV+++AND +YGLA   +T +++R  RV   +E G+ 
Sbjct: 380 DMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDMARTWRVGEKLEYGLI 439

Query: 442 WVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCI 483
            +NS  + +    FGG K+SG GREG  + L+ Y E+K +C+
Sbjct: 440 GINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481


Lambda     K      H
   0.318    0.135    0.406 

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: 524
Number of extensions: 29
Number of successful extensions: 4
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: 485
Length of database: 485
Length adjustment: 34
Effective length of query: 451
Effective length of database: 451
Effective search space:   203401
Effective search space used:   203401
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