GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Streptacidiphilus oryzae TH49

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_152617498.1 BS73_RS04040 aldehyde dehydrogenase family protein

Query= reanno::Smeli:SM_b20891
         (477 letters)



>NCBI__GCF_000744815.1:WP_152617498.1
          Length = 457

 Score =  323 bits (828), Expect = 8e-93
 Identities = 187/455 (41%), Positives = 258/455 (56%), Gaps = 8/455 (1%)

Query: 18  VANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHAILKKTADEILAR 77
           V + NP +  + V E          A +  A  A  AW+ +   +R   L + AD+I A 
Sbjct: 6   VRSTNPHDPSETVAEVPATPTGRFPALLELAGGAGRAWAGTAAPQRAVALTRAADDIAAE 65

Query: 78  KDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSVRPGIGVEITREP 137
              L  L+SRE GK + E  GE VRA + F +FA   L   G+V+P             P
Sbjct: 66  AGRLADLISREVGKPITEARGEVVRAERTFRYFAQTALFPEGDVLPGGEARTLTFTRSRP 125

Query: 138 AGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPKGVL 197
            GVVG+ITPWNFP+AIPAWKLAPAL YGN +V KP+    G + A+ +IL+R  LP GVL
Sbjct: 126 RGVVGLITPWNFPLAIPAWKLAPALAYGNAVVLKPSAQAVGTAEALAEILNRH-LPPGVL 184

Query: 198 NLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQLEMGGKNPFVVLD 257
            L +G G+  G  + +S  + A++FTGST  G++VA A        Q EMGG+NP VVL 
Sbjct: 185 VLAVGPGT--GVLVAESAAISAVSFTGSTEVGRQVAAAVSARGCIAQAEMGGQNPTVVLA 242

Query: 258 DADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVDDALKPGT 317
           DAD+  A+   V SAF   GQ+CTA+SRIIV E +++    A+ E ++ LVV D   P  
Sbjct: 243 DADVDGAIAGIVGSAFAYAGQKCTATSRIIVHEDVYEHTRDALVEAVRALVVLDPSDPKC 302

Query: 318 HIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQPALFTEATNEMRISR 377
            +GPV+D++   +D+   A+    G  L  G +    D PG YL+P L   +  +  ++ 
Sbjct: 303 QVGPVIDEAA--RDSALAAVAASSGRILTGGTKP---DVPGSYLEPTLVEVSDADDVLAT 357

Query: 378 EEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGMVMVNLPT 437
           +E+F PV A++R +    A+ +AN TP+GLS+ + T  L  A    R+  AGM+ VN PT
Sbjct: 358 DEVFAPVTALLRARSVRHAVELANATPYGLSASLYTRDLTAALTHTRDLAAGMIRVNAPT 417

Query: 438 AGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKT 472
            G+D   PFGG K SS+GPREQG  A +FYT   T
Sbjct: 418 TGLDHWAPFGGTKESSFGPREQGLAARQFYTESTT 452


Lambda     K      H
   0.317    0.134    0.391 

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: 601
Number of extensions: 27
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: 477
Length of database: 457
Length adjustment: 33
Effective length of query: 444
Effective length of database: 424
Effective search space:   188256
Effective search space used:   188256
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