GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Pseudovibrio axinellae Ad2

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_068002943.1 PsAD2_RS04510 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_001623255.1:WP_068002943.1
          Length = 363

 Score =  272 bits (696), Expect = 9e-78
 Identities = 156/357 (43%), Positives = 219/357 (61%), Gaps = 6/357 (1%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           M  ++L  + K YGD +VL  INL++++ E  VFVGPSGCGK+T LRMIAGLE ++ G +
Sbjct: 1   MPRIRLENLVKRYGDFEVLHGINLEMEENEFTVFVGPSGCGKTTTLRMIAGLETVSDGEI 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            I    V+ + P  R +AMVFQ YALYPHM V +NMSFAL++ ++ + EID  V   AE 
Sbjct: 61  YIGDRPVSQLEPKARDLAMVFQDYALYPHMNVAKNMSFALRLQRRPRKEIDEKVGLVAEM 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           L L ++L R P  LSGGQRQRVA+GR++ RD   +LFDEPLSNLDA LR   R E+A ++
Sbjct: 121 LGLTKFLHRKPGELSGGQRQRVAMGRALARDAGTFLFDEPLSNLDAKLRCQMRAELAIMR 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + +    M+YVTHDQ+EAMTL  RIVV+ GG I Q G+P EL+++P N+FVA F+GSP M
Sbjct: 181 QKV-RKNMIYVTHDQIEAMTLGDRIVVMNGGYIQQQGTPEELFKQPANKFVAGFLGSPPM 239

Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSL--MGAAVNVGVRPEDMVEAAPGGDY- 297
           N L  KI   G Q  V       A+ +  +  +L    ++V +G+RP D+  +    D+ 
Sbjct: 240 NFLGAKIQDLGGQVFVSGDGFEVALPEERASVALGHSASSVILGIRPSDLHFSPHAPDHE 299

Query: 298 VFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
             + KV ++E +G  ++L      G      +L+       G+  R       +H+F
Sbjct: 300 AIDLKVIVSEYIGAQSVLLCNC--GAQKIEVELKSETPIALGETLRFAVNREAIHLF 354


Lambda     K      H
   0.316    0.135    0.379 

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: 395
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: 373
Length of database: 363
Length adjustment: 30
Effective length of query: 343
Effective length of database: 333
Effective search space:   114219
Effective search space used:   114219
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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