GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pontibacillus litoralis JSM 072002

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_036831855.1 N784_RS02455 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH8
         (254 letters)



>NCBI__GCF_000775615.1:WP_036831855.1
          Length = 507

 Score =  129 bits (323), Expect = 2e-34
 Identities = 78/241 (32%), Positives = 130/241 (53%), Gaps = 13/241 (5%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           ++E+  + K F G+ A  +V L++  GE+  L+G NGAGK+TL N+L G+Y+P +G + +
Sbjct: 4   VIEMLNIRKEFPGIVANNNVNLQVKPGEIHALLGENGAGKSTLMNVLFGLYQPEQGEIKV 63

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122
            G  +N  +P     LG+G   Q+  L    TV +N+++      K  V  +        
Sbjct: 64  KGETVNITNPNVANELGIGMVHQHFMLVDTFTVTENIILGMEPTKKGTVNVA-------- 115

Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182
           K+EKE+K    E+ + + L  D     +++S G Q+R+EI++ L     IL  DEP A +
Sbjct: 116 KAEKEVK----EISERYGLKVDPSAKIQDISVGMQQRVEILKTLYRGADILIFDEPTAVL 171

Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242
            PQE +EL +++  +  E K +I+LI H +  +MEV +R  V+  G  I      +  TN
Sbjct: 172 TPQEISELMDIMGTLVKEGK-SIILITHKLKEIMEVCDRCTVIRKGEGIGTVNVADTSTN 230

Query: 243 K 243
           +
Sbjct: 231 E 231



 Score = 80.5 bits (197), Expect = 6e-20
 Identities = 59/227 (25%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 16  LTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLDGHLLNGKSPYKI 75
           +  V  + L++  GE+VG+ G +G G++ L   + G+     G++TL+G  +   SP K+
Sbjct: 270 INMVKGLNLQVRAGEIVGIAGVDGNGQSELIEAIAGLRNVESGSITLNGKEITNLSPRKV 329

Query: 76  ASLGLGRTFQN---IRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFYKSEKELKAKA 132
              G+    Q+     L  D  + +N+++    + + +     LR    YK       KA
Sbjct: 330 TESGVAHIPQDRHKYGLVLDFPIGENMVLQ-TYYQQPYSKKGVLRYKEIYK-------KA 381

Query: 133 LELLKIFDLDGDAE-TLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGMNPQETAELT 191
             L++ FD+    E TLA++LS G Q++  I R L   P +L   +P  G++      + 
Sbjct: 382 KSLIEEFDVRTPNEYTLARSLSGGNQQKAIIGRELDRSPDLLIAAQPTRGLDVGAIEFIH 441

Query: 192 ELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDE 238
           + +   +D  K  ++L+  +++ +M V++RI V+  G+++A   P E
Sbjct: 442 QRLIEARDSGK-AVLLLSFELDEIMNVSDRIAVMFDGQVVANVLPHE 487


Lambda     K      H
   0.319    0.139    0.385 

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: 311
Number of extensions: 15
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 254
Length of database: 507
Length adjustment: 29
Effective length of query: 225
Effective length of database: 478
Effective search space:   107550
Effective search space used:   107550
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: 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