Alignments for a candidate for HSERO_RS05250 in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Acidovorax sp. GW101-3H11

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_2431 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2431
          Length = 514

 Score =  276 bits (706), Expect = 1e-78
 Identities = 177/509 (34%), Positives = 272/509 (53%), Gaps = 30/509 (5%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           V+ L ++ KRF  ++A D+    LA GEV AL+GENGAGKSTLM IL G Y  D G I +
Sbjct: 4   VLRLSHITKRFGKLVANDSISLTLARGEVLALLGENGAGKSTLMSILFGHYVADEGSIEV 63

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
            G+P+   +PR A A GIG++HQ   L ++L+   N+ +G EP      F    E   + 
Sbjct: 64  FGQPLPPGQPRAALAAGIGMVHQHFTLADNLTVLDNVLLGSEP--LWQPFSRRSEARAKL 121

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
            A+  +  L + P   VG L+V  +Q VEI KAL   + +LI+DEPTA L   E   LF 
Sbjct: 122 LAVSQQFGLPVSPDAKVGSLSVGERQRVEILKALYRGAHILILDEPTAVLTPQESEALFD 181

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
            +  + AQG+ I++ISHK+ E+ +++ RV+V+R GK +A  P Q T+   +   MVG A+
Sbjct: 182 TLAQMVAQGLSIIFISHKLGEVLRVSHRVAVLRQGKLVAEAPAQGTTQGQLAQWMVGHAI 241

Query: 262 DGEQRIP------PDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEV 315
           +  +R P      P  + ++V     G +R   + DVS TLR GEI+  AG+ G G+  +
Sbjct: 242 EAAERRPAQNVGEPICTLSNVSTAPAGRDR---LNDVSLTLRAGEIVAIAGVSGNGQVAL 298

Query: 316 ARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALS 375
           A  + G      G++ + G     + PA  V+ G+  + EDR   G+   + V  N A+S
Sbjct: 299 ADVLCGVRAATTGQVTLRGAPLQAR-PAWLVSQGVARIPEDRHAVGVVGDLPVWEN-AVS 356

Query: 376 SMGR-------FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428
              R       + R  ++ +RA R+ AQ       ++    +  AR LSGGN QK+++ +
Sbjct: 357 ERLRGPWFAHPWFRAFWVKRRAARQHAQRVAETFDVRGGGADAPARSLSGGNMQKLILGR 416

Query: 429 WLLRDCD----------ILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEV 478
            L+   D          ++   +PT G+D+GA   + + L    + G A+++IS +L EV
Sbjct: 417 ALMPPQDAAGNSAPVPQLIVAHQPTWGLDIGAVMFVQQQLINARDSGAAVLLISDDLDEV 476

Query: 479 LRMSHRVLVMCEGRITGELARADATQEKI 507
           L +  RV VM +GR++  L     T+E I
Sbjct: 477 LALGDRVAVMHDGRLSEALPAEGWTREAI 505



 Score = 97.4 bits (241), Expect = 1e-24
 Identities = 69/218 (31%), Positives = 106/218 (48%), Gaps = 6/218 (2%)

Query: 292 VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIG 351
           +S TL +GE+L   G  GAG++ +   +FG    + G I + G       P  A+A GIG
Sbjct: 23  ISLTLARGEVLALLGENGAGKSTLMSILFGHYVADEGSIEVFGQPLPPGQPRAALAAGIG 82

Query: 352 YLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQ 411
            + +   HF LA  + V  N+ L S   +       +R+   A  + V Q      S + 
Sbjct: 83  MVHQ---HFTLADNLTVLDNVLLGSEPLWQP---FSRRSEARAKLLAVSQQFGLPVSPDA 136

Query: 412 QARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMI 471
           +   LS G +Q++ I K L R   IL  DEPT  +       ++  L  +  QG +I+ I
Sbjct: 137 KVGSLSVGERQRVEILKALYRGAHILILDEPTAVLTPQESEALFDTLAQMVAQGLSIIFI 196

Query: 472 SSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQ 509
           S +L EVLR+SHRV V+ +G++  E      TQ ++ Q
Sbjct: 197 SHKLGEVLRVSHRVAVLRQGKLVAEAPAQGTTQGQLAQ 234



 Score = 57.0 bits (136), Expect = 2e-12
 Identities = 60/260 (23%), Positives = 108/260 (41%), Gaps = 21/260 (8%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           P+  L NV     G   L++    L AGE+ A+ G +G G+  L  +L GV    +G + 
Sbjct: 255 PICTLSNVSTAPAGRDRLNDVSLTLRAGEIVAIAGVSGNGQVALADVLCGVRAATTGQVT 314

Query: 81  LDGKPVEITEPRQAQALGIGIIHQE---LNLMNHLSAAQNIFIG--REPRKAMGLFIDED 135
           L G P++   P    + G+  I ++   + ++  L   +N      R P  A   F    
Sbjct: 315 LRGAPLQ-ARPAWLVSQGVARIPEDRHAVGVVGDLPVWENAVSERLRGPWFAHPWFRAFW 373

Query: 136 ELNRQAAAIFARMRLDMD-----PSTPVGELTVARQQMVEIAKALSFDS----------R 180
              R A     R+    D        P   L+    Q + + +AL              +
Sbjct: 374 VKRRAARQHAQRVAETFDVRGGGADAPARSLSGGNMQKLILGRALMPPQDAAGNSAPVPQ 433

Query: 181 VLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIA 240
           +++  +PT  L+   +  + + + + +  G  ++ IS  +DE+  + DRV+VM DG+   
Sbjct: 434 LIVAHQPTWGLDIGAVMFVQQQLINARDSGAAVLLISDDLDEVLALGDRVAVMHDGRLSE 493

Query: 241 TVPMQETSMDTIISMMVGRA 260
            +P +  + + I   M G A
Sbjct: 494 ALPAEGWTREAIGLAMAGAA 513


Lambda     K      H
   0.320    0.135    0.372 

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: 568
Number of extensions: 33
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 4
Length of query: 520
Length of database: 514
Length adjustment: 35
Effective length of query: 485
Effective length of database: 479
Effective search space:   232315
Effective search space used:   232315
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 (21.8 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer

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