GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Hydrogenovibrio halophilus DSM 15072

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_019895416.1 A377_RS12090 ABC transporter ATP-binding protein

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



>NCBI__GCF_000384235.1:WP_019895416.1
          Length = 363

 Score =  176 bits (446), Expect = 9e-49
 Identities = 103/276 (37%), Positives = 164/276 (59%), Gaps = 15/276 (5%)

Query: 21  LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMS----PKD 76
           LK++ L+ID G+   L+GPSGCGK+TL+  IAGL+++  G++ ++  +++       P+ 
Sbjct: 19  LKDVNLRIDPGQIGCLLGPSGCGKTTLLRSIAGLQSVQSGSVTLEGEELTRPGFQKPPEK 78

Query: 77  RDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQL 136
           R I MVFQ +AL+P +SV DN+A+GL  R +   + ++ V  +  L+ +     R P QL
Sbjct: 79  RHIGMVFQDFALFPHLSVADNVAYGL--RDLKGNQRNQRVQELLALVGLPDSGRRYPHQL 136

Query: 137 SGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQ 196
           SGGQQQRVA+ RALA +P + L DEP S LD +LR  +  E++ + +    T + VTH+Q
Sbjct: 137 SGGQQQRVALARALAPKPAVLLLDEPFSGLDVELRESLAREVRHILKSEGMTALMVTHNQ 196

Query: 197 IEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRLL 256
            EA  + D+V VM++G + Q+ TP ++Y+ P + F+A FIG      + +     D  L+
Sbjct: 197 NEAFAMADRVGVMQEGRLLQWDTPYNLYHEPHHAFIADFIGQG----VLITGSVCDCHLV 252

Query: 257 ALLDSGQARCELPLGMQDAGLEDREVILGIRPEQII 292
              + G  +  LPLG Q        V + +RP+ I+
Sbjct: 253 H-TELGLLKAHLPLGSQPG----EAVSVLVRPDDIL 283


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: 359
Number of extensions: 15
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: 363
Length adjustment: 30
Effective length of query: 356
Effective length of database: 333
Effective search space:   118548
Effective search space used:   118548
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 Apr 09 2024. 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