GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Marinobacter adhaerens HP15

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  432 bits (1111), Expect = e-126
 Identities = 225/369 (60%), Positives = 277/369 (75%), Gaps = 4/369 (1%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           M+ LELR++ KTY     +TLK I++ I  GEFLILVGPSGCGKSTLMN IAGLETI+ G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
           +I++D  DIS M PKDRDIAMVFQSYALYPTMSVR+NIAFGLKIR +P  EID+EV RV+
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
            LLQI  L+++KP  LSGGQQQRVAMGRALARRP+IYLFDEPLSNLDAKLRVEMRTE+K 
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           +HQRLKTT VYVTHDQIEAMTL D++AV+KDG +QQ GTPK++Y+ P NLFVA F+GSP 
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 241 MNFIPLRLQRKDGRLLALLDSGQAR-CELPLGMQDAGLEDREVILGIRPEQIILANGEAN 299
           M+F+P+ +++ +G L A +     R  +LP+    A    ++VILGIRPE I     + N
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300

Query: 300 GLPTI---RAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLL 356
               +      ++VTEPTGPD +  + LNDT V CR+ P+     GET  L FD  KV+ 
Sbjct: 301 DQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKVVF 360

Query: 357 FDAKTGERL 365
           FD +T +R+
Sbjct: 361 FDPETEKRI 369


Lambda     K      H
   0.319    0.138    0.393 

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: 485
Number of extensions: 18
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: 386
Length of database: 372
Length adjustment: 30
Effective length of query: 356
Effective length of database: 342
Effective search space:   121752
Effective search space used:   121752
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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