GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Marinobacter guineae M3B

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_099617512.1 CLH62_RS07755 succinylglutamate-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>NCBI__GCF_002744735.1:WP_099617512.1
          Length = 491

 Score =  597 bits (1539), Expect = e-175
 Identities = 288/484 (59%), Positives = 370/484 (76%), Gaps = 1/484 (0%)

Query: 3   LWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62
           L+I+G W+ G G       PV+GE +W G  A+   V+ A R AR AF +W R SFAER 
Sbjct: 8   LFIDGLWLQGHGIPFESVQPVTGETVWDGESANLEDVDAAVREARNAFLKWQRKSFAERQ 67

Query: 63  AVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSE 122
           AVVE F  LLE+NK +L   I  ETGKP WE+ TEV AMI KI IS+KAY+ RTG   S+
Sbjct: 68  AVVEAFGELLEANKEDLAHQIGLETGKPLWESRTEVAAMIGKIGISVKAYNDRTGHSESD 127

Query: 123 MPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMR 182
           +  G A LRHRPHGV+AVFGPYNFPGHLPNGHIVPA+LAGNT++FKPSELTP   E +++
Sbjct: 128 VAGGHAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPAVLAGNTVVFKPSELTPGVAEVIVK 187

Query: 183 LWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242
           LW++AG+P GV+NLVQGG +TG++L++   +DGL FTGS+  G+ LH+Q  GQPEKILAL
Sbjct: 188 LWEKAGIPDGVINLVQGGADTGKSLASHPMIDGLFFTGSSTVGHLLHKQFGGQPEKILAL 247

Query: 243 EMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVS 302
           EMGGNNPLI+ +V D+D AVH  +QSAF++AGQRCTCARRLL+  G +GDAFL RLV V+
Sbjct: 248 EMGGNNPLIVQDVHDLDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDAFLDRLVQVA 307

Query: 303 QRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGI 362
            R+  G +D +PQPF+G +IS +AA +++ A   +   GG+ LL  + L+  T LL+PGI
Sbjct: 308 SRIKVGEFDADPQPFMGSVISAEAADKLLAAQASMLEKGGKSLLEMKSLKPDTGLLSPGI 367

Query: 363 IEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEA 422
           +++TG+  + DEE FGPLL V RY +FD+A+ +AN+TR+GLS G++S +R+ +D+L+ E 
Sbjct: 368 VDVTGLE-LTDEEFFGPLLTVHRYKSFDDALELANDTRYGLSAGILSDDRKLYDRLVEEV 426

Query: 423 RAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLNP 482
           RAGIVNWN+PLTGA+S APFGG+GASGNHRPSA+YAADYCAWPMASLE+    LP TL P
Sbjct: 427 RAGIVNWNRPLTGASSAAPFGGVGASGNHRPSAYYAADYCAWPMASLEAGKSELPDTLAP 486

Query: 483 GLDF 486
           GL+F
Sbjct: 487 GLNF 490


Lambda     K      H
   0.318    0.134    0.412 

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: 843
Number of extensions: 28
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: 492
Length of database: 491
Length adjustment: 34
Effective length of query: 458
Effective length of database: 457
Effective search space:   209306
Effective search space used:   209306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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