GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Neptunomonas antarctica S3-22

Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized)
to candidate WP_054343391.1 Nant_RS19705 betaine-aldehyde dehydrogenase

Query= SwissProt::P56533
         (503 letters)



>NCBI__GCF_001305295.1:WP_054343391.1
          Length = 484

 Score =  514 bits (1325), Expect = e-150
 Identities = 258/459 (56%), Positives = 330/459 (71%), Gaps = 3/459 (0%)

Query: 43  PATGRVLCQMVPCGAEEVDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRERRDNIAK 102
           PATG VL ++      +VD+AV++AQA +L WS M+G ER R+++ A  I+RER D +A 
Sbjct: 25  PATGEVLAEVQQASLADVDKAVEAAQAGFLVWSAMSGAERGRILMRAVAILRERNDELAM 84

Query: 103 LEVINNGKTITEAE-YDIDAAWQCIEYYAGLAPTLSGQHIQLPGGAFAYTRREPLGVCAG 161
           LEV++ GK + EA   DI      IE+YAGLA T+ GQ   L G  F Y+RREPLGVCAG
Sbjct: 85  LEVLDTGKPLQEANCVDIATGADVIEFYAGLAATIHGQQQDLGGTNFYYSRREPLGVCAG 144

Query: 162 ILAWNYPFMIAAWKCAPALACGNAVVFKPSPMTPVTGVILAEIFHEAGVPVGLVNVVQGG 221
           I AWNYP  IA WK  PALA GN ++FKPS  TP++ + LAEIF EAG+P G+ NV+QG 
Sbjct: 145 IGAWNYPIQIAMWKSGPALAAGNCMIFKPSEETPLSVMKLAEIFTEAGLPDGVFNVIQGD 204

Query: 222 AETGSLLCHHPNVAKVSFTGSVPTGKKVMEMSAKTVKHVTLELGGKSPLLIFKDCELENA 281
              G  L  HP +AKVSFTG   TGKKV+  +A ++K VT+ELGGKSPLL+F D +L+NA
Sbjct: 205 YRAGQALSRHPQIAKVSFTGECGTGKKVVADAASSLKQVTMELGGKSPLLVFGDADLDNA 264

Query: 282 VRGALMANFLTQGQVCTNGTRVFVQREIMPQFLEEVVKRTKAIVVGDPLLTETRMGGLIS 341
           V GAL+ANF TQG+VCTNGTRVFV   I  +F+ +VV RT+ +V+GDP    T++G LIS
Sbjct: 265 VSGALLANFYTQGEVCTNGTRVFVHDSIYDEFVSKVVARTERMVIGDPTDLNTQVGALIS 324

Query: 342 KPQLDKVLGFVAQAKKEGARVLCGGEPLTPSDPKLKNGYFMSPCVLDNCRDDMTCVKEEI 401
           +  + KVLGF+  AK  GAR+ CGGE +  +   L  GYF+ P V  +C DDM  VKEEI
Sbjct: 325 EDHMHKVLGFIEAAKTAGARLACGGERVIANG--LDKGYFVQPTVFADCTDDMPNVKEEI 382

Query: 402 FGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYINTYSISP 461
           FGPVMS+L F  EEEV++RAN+T +GLA+GVF+ + SRAHRV A LEAG C+INT+  SP
Sbjct: 383 FGPVMSILRFSDEEEVIRRANDTEYGLAAGVFSTNFSRAHRVIARLEAGICWINTWGASP 442

Query: 462 VEVPFGGYKMSGFGRENGQATVDYYSQLKTVIVEMGDVD 500
            E+P GGYK SG GRENG  T+++Y+Q+K+V VE+GDVD
Sbjct: 443 AEMPVGGYKQSGIGRENGIETLNHYTQIKSVFVELGDVD 481


Lambda     K      H
   0.319    0.135    0.404 

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: 690
Number of extensions: 22
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: 503
Length of database: 484
Length adjustment: 34
Effective length of query: 469
Effective length of database: 450
Effective search space:   211050
Effective search space used:   211050
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 (21.8 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