GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Luteipulveratus mongoliensis MN07-A0370

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_052591230.1 VV02_RS09595 aldehyde dehydrogenase

Query= BRENDA::Q4F895
         (507 letters)



>NCBI__GCF_001190945.1:WP_052591230.1
          Length = 507

 Score =  772 bits (1994), Expect = 0.0
 Identities = 374/507 (73%), Positives = 430/507 (84%)

Query: 1   MTVYARPGTADAIMSFQSRYDNWIGNEWVAPVKGQYFENPTPVTGQNFCDVARSTAEDIE 60
           MTVY RPG++ + ++ + +Y ++IG E+VAP KG+YFEN  P TG+ F  V R TAEDIE
Sbjct: 1   MTVYERPGSSGSKIAVEDKYGHYIGGEFVAPKKGEYFENYAPQTGEVFTQVGRGTAEDIE 60

Query: 61  LALDAAHAAAPAWGKTSVAERAIILNKIADRMEENLESIALAESWDNGKPIRETLNADIP 120
            ALDAAH AA  WG TS AERA +L KIADR+E+NLE +A+ ESWDNGK +RETL AD+P
Sbjct: 61  AALDAAHNAADKWGTTSPAERAGVLLKIADRIEKNLEDLAVIESWDNGKAVRETLAADLP 120

Query: 121 LAIDHFRYFAGAIRAQEGSLSEINSDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPAL 180
           LA+DHFRYFAGA+RAQEG +SEI+ +T+AYHFHEPLGVVGQIIPWNFPILMA WKLAPAL
Sbjct: 121 LAVDHFRYFAGALRAQEGGVSEIDENTIAYHFHEPLGVVGQIIPWNFPILMATWKLAPAL 180

Query: 181 AAGNAIVLKPAEQTPVSILHLIGIIGDLLPAGVLNIVNGFGVEAGKPLASSPRIKKIAFT 240
           AAGNA+VLKPAEQTP SIL +I +IGDLLP GVLNIVNGFG EAGKPLAS+ R+ K+AFT
Sbjct: 181 AAGNAVVLKPAEQTPWSILKVIELIGDLLPPGVLNIVNGFGTEAGKPLASNKRVAKVAFT 240

Query: 241 GETTTGRLIMQYASQNLIPVTLELGGKSPNIFFSDVLASNDDYQDKALEGFTMFALNQGE 300
           GETTTGRLIMQYASQN+IPVTLELGGKSPN+FF DV A  D + DKA EGF MFALNQGE
Sbjct: 241 GETTTGRLIMQYASQNIIPVTLELGGKSPNVFFEDVAAERDAFYDKAQEGFAMFALNQGE 300

Query: 301 VCTCPSRSLIQEDIFDEFLAMAAIRTKAVRQGDPLDTDTMIGAQASNDQLEKILSYIEIG 360
           VCTCPSR+L+Q  I+ +F+  A  R + ++ G+PLDT+T +GAQASNDQLEKI SY++IG
Sbjct: 301 VCTCPSRALVQSSIYSDFMKDAVARVEKIKMGNPLDTETTMGAQASNDQLEKIKSYLDIG 360

Query: 361 KAEGAKVITGGERAELGGDLSGGYYVQPTVFTGNNKMRIFQEEIFGPVVSVTSFKDYDEA 420
           K EGAKV+TGGE A+L GDL+GGYYVQPTVF G+N MRIFQEEIFGPVVSVT F D  +A
Sbjct: 361 KREGAKVLTGGEEAKLEGDLAGGYYVQPTVFEGDNSMRIFQEEIFGPVVSVTPFNDEADA 420

Query: 421 IEIANDTLYGLGAGVWSRDGGVAYRAGRDIQAGRVWTNTYHQYPAHAAFGGYKQSGIGRE 480
           ++ ANDTLYGLGAGVWSRDG  AYR GR I+AGRVWTN YH YPAHAAFGGYKQSGIGRE
Sbjct: 421 LKTANDTLYGLGAGVWSRDGARAYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRE 480

Query: 481 NHLMMLSHYQQTKNLLVSYAQKAQGFF 507
           NH MML HYQQTKNLLVSY+Q AQGFF
Sbjct: 481 NHKMMLDHYQQTKNLLVSYSQDAQGFF 507


Lambda     K      H
   0.318    0.135    0.401 

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: 831
Number of extensions: 21
Number of successful extensions: 1
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: 507
Length of database: 507
Length adjustment: 34
Effective length of query: 473
Effective length of database: 473
Effective search space:   223729
Effective search space used:   223729
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: 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