GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Acidovorax sp. GW101-3H11

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_609
          Length = 505

 Score =  374 bits (961), Expect = e-108
 Identities = 211/506 (41%), Positives = 327/506 (64%), Gaps = 22/506 (4%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDA--GEI 71
           +L+ + I K FPGVVA++ V+ +V   EI +++GENGAGKSTL+K+L+GV    +  G+I
Sbjct: 2   LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61

Query: 72  LVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDEN 131
           L +G+  EF    D+   GI +IHQEL L   +++AENIFL  E  R         +D  
Sbjct: 62  LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETAR------HGVIDWM 115

Query: 132 YMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEE 191
             ++R++ LL  +G   SPD  V  L   ++Q+VEI KAL ++ R++ +DEPT+SL   +
Sbjct: 116 AAHSRAQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNEND 175

Query: 192 TERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGEL--KKGEFDVDTII 249
           ++ L +++  LK++GI+ + +SH+L+E+ R++D I V+RDG  +  L  ++G    D +I
Sbjct: 176 SQALLDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVI 235

Query: 250 KMMVGREVEFFPHGIETRPGEIALEVRNLKW-------KDKVKNVSFEVRKGEVLGFAGL 302
           + MVGRE+       + + GEI  EVRN +        ++ +K +   VR+GE++G AGL
Sbjct: 236 QAMVGREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGL 295

Query: 303 VGAGRTETMLLVFGVN--QKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLR 360
           +GAGRTE  + +FG +  Q+ SG++ ++G+ +++   E A+  G+  + EDRK  GLVL 
Sbjct: 296 MGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLN 355

Query: 361 MTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKV 420
             ++ N  L +L  +S +  V+D  +E  +++DY ++L I+   + Q T NLSGGNQQKV
Sbjct: 356 EDIQFNTSLANLPGVS-FASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKV 414

Query: 421 VLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDR 480
           VL+KWL T+ ++LI DEPTRGIDVGAK EI+ +I +LAA+GK VI+ISSE+PE+L ++DR
Sbjct: 415 VLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDR 474

Query: 481 IVVMWEGEITAVLDNREKRVTQEEIM 506
           I VM EG   A +   E   +QE+IM
Sbjct: 475 IYVMNEGRFVAEMPTSE--ASQEKIM 498



 Score = 82.4 bits (202), Expect = 4e-20
 Identities = 68/247 (27%), Positives = 127/247 (51%), Gaps = 13/247 (5%)

Query: 273 LEVRNLKWKDK----VKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGV--NQKESGDIY 326
           LE+RN++        +  V+ +V+ GE+    G  GAG++  M ++ GV  +   SG I 
Sbjct: 3   LEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQIL 62

Query: 327 VNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERK 386
            +G++ E     D+  +GI +I ++  L  L   +++ +NI L +  + +R G V+D   
Sbjct: 63  FDGQEREFAGIRDSEHLGIIIIHQELALVPL---LSIAENIFLGN--ETARHG-VIDWMA 116

Query: 387 EEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGA 446
               ++  + ++ +       + + L  G QQ V +AK L+    +LI DEPT  ++   
Sbjct: 117 AHSRAQALLHKVGLGESPDTPVGQ-LGVGKQQLVEIAKALSRKVRLLILDEPTASLNEND 175

Query: 447 KAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLDNREKRVTQEEIM 506
              +  ++ EL AQG   I+IS +L EI  ++D I V+ +G    +LD RE  V+++ ++
Sbjct: 176 SQALLDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVI 235

Query: 507 YYASGQK 513
               G++
Sbjct: 236 QAMVGRE 242



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 51/224 (22%), Positives = 109/224 (48%), Gaps = 4/224 (1%)

Query: 33  VDFEVYENEIVSLIGENGAGKSTLIKILTGVL--KPDAGEILVNGERVEFHSPVDAFKKG 90
           +D  V   EIV + G  GAG++ L   + G    +  +GE+ ++G+ ++  +   A   G
Sbjct: 280 IDLNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHG 339

Query: 91  ISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFSP 150
           ++ + ++    + + + E+I            + +S +D    +  +++  + +  + S 
Sbjct: 340 LAYVTEDRK-GNGLVLNEDIQFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSG 398

Query: 151 -DALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGISV 209
            D    NL+   +Q V + K L   P ++ +DEPT  + V     ++ +I  L + G  V
Sbjct: 399 VDQKTLNLSGGNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCV 458

Query: 210 VFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
           + +S  + E++ I+DRI VM +G+ + E+   E   + I++ +V
Sbjct: 459 IVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEKIMRAIV 502


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: 678
Number of extensions: 38
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 520
Length of database: 505
Length adjustment: 35
Effective length of query: 485
Effective length of database: 470
Effective search space:   227950
Effective search space used:   227950
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 17 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