GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Pseudovibrio axinellae Ad2

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  284 bits (726), Expect = 6e-81
 Identities = 169/506 (33%), Positives = 293/506 (57%), Gaps = 25/506 (4%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L  + I K F  +VA  NV+ +++  EIV+L+GENGAGK+TL+ IL G    D G ++V
Sbjct: 10  LLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMV 69

Query: 74  ---NGERVEFH--SPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRV 128
              +G  V+    +P  A + GI ++HQ   L +N+T  ENI L  E++  +K + S   
Sbjct: 70  RTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSKA- 128

Query: 129 DENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLT 188
                  + +EL+   G +   D  V  L   +RQ VEI KAL ++ RI+ +DEPT+ LT
Sbjct: 129 -----RAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLT 183

Query: 189 VEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTI 248
            +E++ LF  +++L ++G++++F+SH++ EV+  SDR+ V+R G+ + +L   + D   +
Sbjct: 184 PQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKL 243

Query: 249 IKMMVGREVEFFPHGIETRPGEIALEVRNLK------WKDKVKNVSFEVRKGEVLGFAGL 302
            ++MVG  V+      E  PG    E+   K       ++ ++NV+  +RKGE++G AG+
Sbjct: 244 AELMVGHAVQM----AEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGV 299

Query: 303 VGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMT 362
            G G++    ++ G+ +  +G + +  + ++  N   AI+ G+  IPEDR   G+V  M+
Sbjct: 300 SGNGQSMLAKVLSGLEEPTAGAVTLGSQPLK-ANAAAAIQSGVARIPEDRHHDGIVGAMS 358

Query: 363 VKDNIVLPSLKK--ISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKV 420
           V++N+VL  ++K    R+GL L   +  + +++ +K   I+      ++  LSGGN QK+
Sbjct: 359 VEENLVLEEIRKPAYQRFGL-LRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKI 417

Query: 421 VLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDR 480
           VLA+ L     I++  +P+RG+DVGA A++HR ++E   +G  V++IS +L E+  LSDR
Sbjct: 418 VLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDR 477

Query: 481 IVVMWEGEITAVLDNREKRVTQEEIM 506
           I V+  G ++  + + E    Q  +M
Sbjct: 478 IAVIHRGHVSEPMASEELDKKQVGLM 503



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 68/250 (27%), Positives = 125/250 (50%), Gaps = 8/250 (3%)

Query: 13  EILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEIL 72
           EIL  KG V    G   ++NV+  + + EI+ L G +G G+S L K+L+G+ +P AG + 
Sbjct: 265 EILVFKG-VSAGEGRELIENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGLEEPTAGAVT 323

Query: 73  VNGERVEFHSPVDAFKKGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVD 129
           +  + ++ ++   A + G++ I ++ +   +   M+V EN+ L  E +R         + 
Sbjct: 324 LGSQPLKANAAA-AIQSGVARIPEDRHHDGIVGAMSVEENLVL--EEIRKPAYQRFGLLR 380

Query: 130 ENYMYTRSKELLDLIGAKFS-PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLT 188
            N +  R++E +     + S P A+ R L+    Q + + + L +EP I+   +P+  L 
Sbjct: 381 FNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLD 440

Query: 189 VEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTI 248
           V  T  +   ++  + RG  V+ +S  LDE+ ++SDRI V+  G     +   E D   +
Sbjct: 441 VGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQV 500

Query: 249 IKMMVGREVE 258
             MM G   +
Sbjct: 501 GLMMAGHSAK 510


Lambda     K      H
   0.319    0.138    0.381 

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: 629
Number of extensions: 40
Number of successful extensions: 10
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: 520
Length of database: 515
Length adjustment: 35
Effective length of query: 485
Effective length of database: 480
Effective search space:   232800
Effective search space used:   232800
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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