GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Geotalea uraniireducens Rf4

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011938485.1 GURA_RS08035 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000016745.1:WP_011938485.1
          Length = 475

 Score =  286 bits (732), Expect = 1e-81
 Identities = 167/475 (35%), Positives = 267/475 (56%), Gaps = 17/475 (3%)

Query: 4   HQNLIAGEWVGGD--GVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGIL 61
           ++ LI GEW G D  G+  INP + D ++G    A+AED +AAI +A+  F   S     
Sbjct: 5   YRMLIGGEWSGDDRTGIEVINPYD-DSLIGIVPEATAEDVEAAIVSARKGFDEISAMPAY 63

Query: 62  ERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEV 121
           +R  IL++ ++ I+  K+E+  +++RE GK+    + E  R+ + F+F A E     GE+
Sbjct: 64  KRSEILERASEFIMRDKEEIAGIIAREAGKSWKYALAEAERSAETFKFAAIEARASHGEI 123

Query: 122 VPS----VRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVP 177
           VP     V  G      R P G++G ITP+NFP+ + A KLAPA+  GN +V KPA   P
Sbjct: 124 VPMDASPVSAGRFGFYLRNPIGIIGAITPFNFPLNLVAHKLAPAIATGNAVVLKPATKTP 183

Query: 178 GCSWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASV 237
             S  + ++L  AGLP G LN+++G G+ VG  +++   +  ITFTGS   G+   + S 
Sbjct: 184 LTSLKLAELLMEAGLPAGALNVIIGSGATVGNRLVEDERLAMITFTGSPPVGR--GIKSR 241

Query: 238 EHNRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFV 297
              ++  LE+G  +P ++ +D D+  AV   V  +F ++GQ C +  RI V +  ++ F+
Sbjct: 242 SGLKRVTLELGSNSPTIIEEDGDVDKAVSRCVIGSFANSGQVCISVQRIFVHQSRYEEFI 301

Query: 298 AAMGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTP 357
           A   E  + L V D       IGP++ + +L +   ++   K+ GA +A GG V+     
Sbjct: 302 AKFVEATRSLKVGDPFDKTCDIGPMISRKELERAVSWLEEAKKLGAVIAVGGNVV----- 356

Query: 358 GFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLK 417
           G  L+P + T  T +M++   E+F P+ +V+  K +DEAL +A+D+ +GL +GI T+ + 
Sbjct: 357 GNCLEPTVLTSVTRDMQVMCSEVFAPIVSVLPYKTFDEALEMADDSIYGLQAGIYTSDIN 416

Query: 418 HATHFKRNAEAGMVMVN-LPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVK 471
            A    +  + G V++N +PT  VD H+P+GG K S  G RE  +YA E  TN+K
Sbjct: 417 KAFKAVKRLDVGGVIINDVPTFRVD-HMPYGGNKESGLG-REGVRYAMEEMTNIK 469


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: 536
Number of extensions: 29
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: 477
Length of database: 475
Length adjustment: 33
Effective length of query: 444
Effective length of database: 442
Effective search space:   196248
Effective search space used:   196248
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 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