GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Novosphingobium fuchskuhlense FNE08-7

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate WP_082697952.1 AQZ52_RS13580 NAD-dependent succinate-semialdehyde dehydrogenase

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



>NCBI__GCF_001519075.1:WP_082697952.1
          Length = 475

 Score =  551 bits (1421), Expect = e-161
 Identities = 279/454 (61%), Positives = 336/454 (74%), Gaps = 1/454 (0%)

Query: 28  VAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRALTAKERGAKLRRWFELLNENS 87
           +A+ NPATGA+IA V     AE  A I AA+AA PAW A TAK R A LRRW+ L+ E  
Sbjct: 17  LAVHNPATGALIATVRDYAPAEIAAIIDAADAARPAWAAETAKARAAVLRRWYALIMERQ 76

Query: 88  DDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEEAKRIYGDTIPGHQGDKRIMVIKQPV 147
           ++LA L+T+E GKPL EA+GEV Y ASFIEWFAEEAKR YG+T+P     KR++ IKQPV
Sbjct: 77  EELAALITAECGKPLAEARGEVAYGASFIEWFAEEAKRAYGETVPTFAVGKRVLTIKQPV 136

Query: 148 GVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALALAVLAERAGIPAGVFS 207
           G  AAITPWNFP AMITRK  PALAAGC++VVKPA  TP +ALAL  LA  AG+PA +F 
Sbjct: 137 GTCAAITPWNFPIAMITRKVGPALAAGCSIVVKPAEATPLSALALETLAREAGVPADLFR 196

Query: 208 VI-TGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLMAQCAPTLKKLSLELGGNAPFIVFD 266
           V  + D   +G   C +P VRKLSFTGST VG  LMAQ A  + +LSLELGGNAPFIVFD
Sbjct: 197 VTPSNDPAGVGALFCHHPKVRKLSFTGSTRVGKILMAQAAENVTRLSLELGGNAPFIVFD 256

Query: 267 DANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAEKLSMAVAKLKVGEGIIAGV 326
           DA++DAA +G M +K+RNAGQTCVCANR+ VQ  V+D F E+L   VA L VG+G   G 
Sbjct: 257 DADLDAAADGLMASKFRNAGQTCVCANRVLVQDSVHDAFVERLRAKVAALVVGDGAAPGT 316

Query: 327 TTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHELGGNFFEPTVLTNADKSMRVAREE 386
           T GPLINAAAVEKV+S + DA+  GAT L GG   ++G +FFEPTVL   +  M +A  E
Sbjct: 317 TIGPLINAAAVEKVESLVGDALAGGATALMGGHRSDVGASFFEPTVLAGVNPQMAIATSE 376

Query: 387 TFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDISLVWKVAESLEYGMVGVNTGLIS 446
            FGP+ PL +F D D  ++ ANDT FGLAAYF+ RD+  VW+V E+LEYGMVGVN G+IS
Sbjct: 377 IFGPVVPLIRFKDEDQAVRIANDTPFGLAAYFFARDLGRVWRVMEALEYGMVGVNDGIIS 436

Query: 447 TEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICM 480
           TEVAPFGG+K SGLGREGS++G++EYLE+KY  M
Sbjct: 437 TEVAPFGGIKQSGLGREGSRHGLDEYLELKYCLM 470


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: 634
Number of extensions: 22
Number of successful extensions: 2
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: 475
Length adjustment: 34
Effective length of query: 448
Effective length of database: 441
Effective search space:   197568
Effective search space used:   197568
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: 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