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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_609 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources