GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pontibacter ramchanderi LP43

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_101443649.1 BD749_RS06040 ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>NCBI__GCF_002846395.1:WP_101443649.1
          Length = 317

 Score =  141 bits (356), Expect = 2e-38
 Identities = 105/310 (33%), Positives = 151/310 (48%), Gaps = 30/310 (9%)

Query: 23  VLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVG----MPPR 78
           VL  +       E L + G +G GKSTLL  IAGL +P+ G+I   GK V+G    + P 
Sbjct: 8   VLHGISFRQGEYEKLAIAGETGSGKSTLLQAIAGLVQPSAGQITFEGKRVIGPHDKLVPG 67

Query: 79  DRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQ 138
              IA + Q Y L   L V   + +A     + + +  + + EV    +ISHL  R+  Q
Sbjct: 68  HEGIAYLSQHYDLPQFLRVEQVLRYA----NILQGDEAETLYEVC---RISHLKQRKTHQ 120

Query: 139 LSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHD 198
           LSGG+RQR+A+ R L+  P L L DEP SNLD   +  ++  I  + +   IT + ++HD
Sbjct: 121 LSGGERQRIALARLLSTWPSLLLLDEPYSNLDKGHKELLKEVIHDITERLAITCILISHD 180

Query: 199 QVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAVT---GGQ 255
             + ++   RI ++KGG + Q GTP+++Y  P + Y A   G+   NL+   V      +
Sbjct: 181 PHDTLSWADRILIIKGGRMVQQGTPEQVYRHPVDAYTAGLFGN--YNLIPAHVALPFAEK 238

Query: 256 FGIQGAALNLAPPPSSANEVLLGVRPEH--LVMQETAPWRGRVSVVEPTGPDTYVMVDTA 313
            GI   A +L             VRPEH   V +E     G V  V   G    V V   
Sbjct: 239 LGIAVTARDLL------------VRPEHFRFVAKEAGSLNGTVQKVTFFGGYYDVQVQVT 286

Query: 314 AGSVTLRTDA 323
             SVT+RT A
Sbjct: 287 GFSVTVRTQA 296


Lambda     K      H
   0.318    0.135    0.388 

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: 251
Number of extensions: 7
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: 355
Length of database: 317
Length adjustment: 28
Effective length of query: 327
Effective length of database: 289
Effective search space:    94503
Effective search space used:    94503
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: 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