GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Tistlia consotensis USBA 355

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_179243903.1 B9O00_RS00790 aldehyde dehydrogenase family protein

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



>NCBI__GCF_900177295.1:WP_179243903.1
          Length = 480

 Score =  687 bits (1773), Expect = 0.0
 Identities = 347/479 (72%), Positives = 395/479 (82%), Gaps = 3/479 (0%)

Query: 1   MTLHQNLIAGEWVGGDGVA-NINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSG 59
           MT+H NLIAGEWV     + N NPS+  DVVG YA+  A  A  AI AA AAFPAWSRS 
Sbjct: 1   MTMHANLIAGEWVDAPNASENRNPSDLSDVVGLYAQGDAAQAGQAIDAAAAAFPAWSRST 60

Query: 60  ILERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAG 119
             +R  IL     EILARK+ELGRLLSREEGKTL EGIGETVRAGQIF+FFAGE LR+AG
Sbjct: 61  PQQRFDILDAAGTEILARKEELGRLLSREEGKTLPEGIGETVRAGQIFKFFAGEALRIAG 120

Query: 120 EVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGC 179
           + + S RPG+  E TREP GVVG+ITPWNFPIAIPAWKLAPAL +GN +V KPA+LVPGC
Sbjct: 121 DRIDSTRPGVIAEATREPLGVVGLITPWNFPIAIPAWKLAPALAFGNCVVMKPADLVPGC 180

Query: 180 SWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEH 239
           +WA+ DIL RAGLPKGV NLVMG+GSVVG+A+L SP V AI+FTGS ATG+ VA   +E 
Sbjct: 181 AWALADILQRAGLPKGVFNLVMGRGSVVGEAILASPKVAAISFTGSVATGRHVARRCIEG 240

Query: 240 N--RKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFV 297
              +K+QLEMGGKNPFVVLDDADL VA  +A+N AFFSTGQRCTASSR+IVTEGIHDRFV
Sbjct: 241 EAMKKFQLEMGGKNPFVVLDDADLEVAANSALNGAFFSTGQRCTASSRLIVTEGIHDRFV 300

Query: 298 AAMGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTP 357
            A+  ++K L VD+ALK GT IGPVVDQ QL+QD DYI +G+ EGAKLA+GGE ++R+T 
Sbjct: 301 EALTSKLKALKVDNALKEGTQIGPVVDQRQLDQDLDYIKVGQDEGAKLAWGGERLNRETE 360

Query: 358 GFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLK 417
           GFYLQPALFTE  N MRI+REEIFGPVA+VIRVKDYD ALAVANDT FGLS+GIAT+SLK
Sbjct: 361 GFYLQPALFTETDNAMRINREEIFGPVASVIRVKDYDSALAVANDTQFGLSAGIATSSLK 420

Query: 418 HATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTL 476
           HA HFKRN++AGMVMVNLPTAGVD+HVPFGGRK SSYG REQG+YA EFYT VKTAY +
Sbjct: 421 HAEHFKRNSQAGMVMVNLPTAGVDYHVPFGGRKNSSYGAREQGRYAVEFYTTVKTAYAM 479


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: 739
Number of extensions: 21
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: 477
Length of database: 480
Length adjustment: 34
Effective length of query: 443
Effective length of database: 446
Effective search space:   197578
Effective search space used:   197578
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.

Links

Downloads

Related tools

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