GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Phaeobacter inhibens BS107

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD

Query= reanno::MR1:200453
         (482 letters)



>FitnessBrowser__Phaeo:GFF2918
          Length = 491

 Score =  617 bits (1592), Expect = 0.0
 Identities = 311/482 (64%), Positives = 376/482 (78%), Gaps = 2/482 (0%)

Query: 2   LLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAAL 61
           LL DPSLL  + YI G + D  +  T A+ NPA G VIA V  + +++   AIA AE A 
Sbjct: 11  LLTDPSLLEPRAYIGGAFVDG-ADGTFAVKNPARGDVIANVADVSRSQVAGAIAQAEVAQ 69

Query: 62  PAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAE 121
             W   T KER   LR+WF+L+ EN +DLA+++T+E GKPL E++GE+ Y ASFIE+FAE
Sbjct: 70  KDWAKWTGKERANVLRKWFDLMMENQEDLAVILTAEMGKPLAESRGEIGYGASFIEFFAE 129

Query: 122 EAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKP 181
           EAKRIYG+TIPGHQ DKRI V+KQP+GV A+ITPWNFP AMITRKA PALAAGC  V +P
Sbjct: 130 EAKRIYGETIPGHQRDKRITVLKQPIGVAASITPWNFPNAMITRKAGPALAAGCAFVARP 189

Query: 182 APQTPFTALALAVLAERAGIPAGVFSVITG-DAIAIGNEMCTNPIVRKLSFTGSTNVGIK 240
           A  TP +A ALAVLA+RAGIPAGVF+V+T  +A   G E C N  VRKL+FTGST VG  
Sbjct: 190 AELTPLSATALAVLADRAGIPAGVFNVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRI 249

Query: 241 LMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300
           LM Q A T+ K S+ELGGNAPFIVFDDA++DAAVEGA++ K+RN GQTCVCANRIYVQAG
Sbjct: 250 LMRQAADTVMKCSMELGGNAPFIVFDDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAG 309

Query: 301 VYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKV 360
           VYD FA KL  AVAK+ VG+G+  G   GPLIN  AVEKVQ+H+ DA +KGA V+ GG  
Sbjct: 310 VYDAFAAKLKEAVAKMTVGDGLAEGTQFGPLINEKAVEKVQAHIADAKEKGAEVILGGNP 369

Query: 361 HELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYG 420
            ELGG FFEPT++T A + M  +++ETFGP+APLFKF   DDVI+ ANDT FGLA+YFY 
Sbjct: 370 SELGGTFFEPTIITGATQDMVFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYA 429

Query: 421 RDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICM 480
           +D+S V+KVAE+LEYG+VGVNTG+ISTE+APFGG+K SGLGREGS +GIE+YLE+KYICM
Sbjct: 430 KDLSRVYKVAEALEYGIVGVNTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYICM 489

Query: 481 SV 482
           SV
Sbjct: 490 SV 491


Lambda     K      H
   0.318    0.133    0.390 

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: 674
Number of extensions: 19
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: 482
Length of database: 491
Length adjustment: 34
Effective length of query: 448
Effective length of database: 457
Effective search space:   204736
Effective search space used:   204736
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 Sep 17 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