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_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_607 Predicted
           L-arabinose ABC transport system, ATP-binding protein
          Length = 517

 Score =  349 bits (896), Expect = e-100
 Identities = 192/477 (40%), Positives = 302/477 (63%), Gaps = 10/477 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L+  GI K+F G+  + +V   +Y  EI +L+G+NGAGKSTLIK+LTGVL+   G++ +
Sbjct: 18  VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            G+ V   SP+ A + GIS ++QE+NLC N++VAENIF       G  +    R+D   +
Sbjct: 78  GGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGF--RIDWATL 135

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
           + R+++L+  IG +     L+ +   A +Q+V I +AL  E R++ +DEPTSSL  +E +
Sbjct: 136 HQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQ 195

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
           +LFE++  L+S G+S+VFV+H L++V  +SDRI V+R+G  +GE    +     +I  M+
Sbjct: 196 KLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAML 255

Query: 254 GREVEFFPH------GIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGR 307
           GR++            +++R   + L+   L    +++ +  ++R GEV+G AGL+G+GR
Sbjct: 256 GRDLAAASEQPAPAPAVDSRHANL-LQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGR 314

Query: 308 TETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNI 367
           TE   L+FG+ Q + G + ++G+ V+  NP DAI+ G+ L PE+RK  G+V  ++V++NI
Sbjct: 315 TELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENI 374

Query: 368 VLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLA 427
            L +L+     G  L   ++ E++E YVK L IKT ++ +    LSGGNQQK +LA+W+A
Sbjct: 375 AL-ALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMA 433

Query: 428 TNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVM 484
               +LI DEPTRGIDV AK EI   I  LA  G AV+ ISSE+ E++ ++ RIVV+
Sbjct: 434 IEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVL 490



 Score =  113 bits (283), Expect = 1e-29
 Identities = 65/212 (30%), Positives = 124/212 (58%), Gaps = 6/212 (2%)

Query: 33  VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92
           +D ++   E+V L G  G+G++ L ++L G+ +PD G + ++G+ V+F +P+DA + G++
Sbjct: 294 LDLQIRAGEVVGLAGLLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLA 353

Query: 93  VIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFS 149
           +  +E     +   ++V ENI LA +A  G  + LS R ++  +  R  +LL +     +
Sbjct: 354 LCPEERKTDGIVAELSVRENIALALQARMGVGKFLS-RSEQTELAERYVKLLGI--KTET 410

Query: 150 PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGISV 209
            D  +  L+   +Q   + + +  EPR++ +DEPT  + V   + + + I  L   G++V
Sbjct: 411 VDKPIGLLSGGNQQKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAV 470

Query: 210 VFVSHRLDEVMRISDRIVVMRDGKRIGELKKG 241
           +F+S  + EV+R++ RIVV+RD +++GEL  G
Sbjct: 471 LFISSEMSEVVRVAHRIVVLRDRRKVGELPAG 502



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 49/210 (23%), Positives = 104/210 (49%), Gaps = 9/210 (4%)

Query: 284 VKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKM 343
           +++V   +  GE+    G  GAG++  + ++ GV +   G + + G+ V   +P  A ++
Sbjct: 34  LRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLGGQAVWPDSPLAAQRL 93

Query: 344 GIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKIS-RWGLVLDERKEEEISEDYVKRLSIKT 402
           GI  + ++     L   ++V +NI      +     G  +D     + + D V R+ ++ 
Sbjct: 94  GISTVYQE---VNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQRARDLVARIGLQI 150

Query: 403 PSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGK 462
             + ++  +     QQ V +A+ L+  + +LI DEPT  +D     ++  ++R L ++G 
Sbjct: 151 -DVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQKLFEVLRRLRSEGL 209

Query: 463 AVIMISSELPEILNLSDRIVVM----WEGE 488
           +++ ++  L ++  +SDRI V+    W GE
Sbjct: 210 SIVFVTHFLNQVYAVSDRITVLRNGSWVGE 239


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: 593
Number of extensions: 25
Number of successful extensions: 8
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: 517
Length adjustment: 35
Effective length of query: 485
Effective length of database: 482
Effective search space:   233770
Effective search space used:   233770
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 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