Alignments for a candidate for HSERO_RS05250 in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Phyllobacterium brassicacearum STM 196

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_106709787.1 CU102_RS04475 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_003010955.1:WP_106709787.1
          Length = 514

 Score =  420 bits (1079), Expect = e-122
 Identities = 235/497 (47%), Positives = 323/497 (64%), Gaps = 9/497 (1%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           PV+++RNV K F  V AL N  F L  GEVHAL GENGAGKSTLM I++GV Q D G+I+
Sbjct: 4   PVLSIRNVTKHFGAVKALTNVNFALERGEVHALCGENGAGKSTLMNIIAGVLQPDEGEIV 63

Query: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140
           LDGK V I  P  AQ+LG+G++HQE+ L    S A+NIF+    R+   L ++  +L R+
Sbjct: 64  LDGKTVRIGSPAAAQSLGLGLVHQEIALCPDASVAENIFMASISRQR-SLLMNYRKLERE 122

Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200
           A A+ +R+   +D    VGEL ++ QQ+VEIAKAL+ D RVLI DEPTAAL  AE   LF
Sbjct: 123 AQAVMSRLA-PIDVRRKVGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTEAEARILF 181

Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260
            IIRDL+A G+ IVYISH+M E+ ++ DRV+V+RDG+Y++T  + + + D ++  MVGR 
Sbjct: 182 EIIRDLKANGISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVVRRMVGRE 241

Query: 261 LDGEQRIPPDTSR----NDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVA 316
           +   Q  PP         +VV  VRGL      RDV   L +GEILG  GL+G+GRTE+A
Sbjct: 242 I--TQLYPPKQPAGERPQEVVFSVRGLGDNERFRDVDIDLTRGEILGIGGLIGSGRTEIA 299

Query: 317 RAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376
             I G      G+I+IHG +  I + ADAV  G+ YLSEDRK  GL + + +  NI++ +
Sbjct: 300 EGICGLRATTNGQILIHGKQQAIGTYADAVKAGLVYLSEDRKGSGLFLDLSIAKNISVLN 359

Query: 377 MGRFT-RVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCD 435
           +   T  +G +D     + A+ + ++L I+  S+      LSGGNQQK+ IAK L     
Sbjct: 360 LDALTGHLGLIDTVGEGDLARDFAQRLNIRMGSIGAPVSSLSGGNQQKVAIAKQLAIQPK 419

Query: 436 ILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITG 495
           ++  DEPTRGIDVGAKSEI+ LL  LA+ G  I++ISSELPE+L +  RV+V+ EG + G
Sbjct: 420 VILMDEPTRGIDVGAKSEIHALLRELAQSGIGIIVISSELPELLGLCDRVIVIREGEVAG 479

Query: 496 ELARADATQEKIMQLAT 512
           EL   D T+E++++LA+
Sbjct: 480 ELGMDDMTEERVIRLAS 496



 Score = 99.8 bits (247), Expect = 2e-25
 Identities = 72/243 (29%), Positives = 120/243 (49%), Gaps = 10/243 (4%)

Query: 277 VLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           VL +R + +     +A+ +V+F L +GE+    G  GAG++ +   I G    + GEI++
Sbjct: 5   VLSIRNVTKHFGAVKALTNVNFALERGEVHALCGENGAGKSTLMNIIAGVLQPDEGEIVL 64

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIR 392
            G    I SPA A + G+G + ++     L     V  NI ++S+ R  R   M+ R + 
Sbjct: 65  DGKTVRIGSPAAAQSLGLGLVHQE---IALCPDASVAENIFMASISR-QRSLLMNYRKLE 120

Query: 393 EAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKS 452
             AQ  + +LA     V ++   L   +QQ + IAK L  DC +L FDEPT  +      
Sbjct: 121 REAQAVMSRLA--PIDVRRKVGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTEAEAR 178

Query: 453 EIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLAT 512
            +++++  L   G +IV IS  + E+  +  RV V+ +GR       AD T + +++   
Sbjct: 179 ILFEIIRDLKANGISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVVRRMV 238

Query: 513 QRE 515
            RE
Sbjct: 239 GRE 241



 Score = 88.2 bits (217), Expect = 7e-22
 Identities = 64/223 (28%), Positives = 113/223 (50%), Gaps = 11/223 (4%)

Query: 44  ELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIH 103
           +L  GE+  + G  G+G++ + + + G+    +G IL+ GK   I     A   G+  + 
Sbjct: 278 DLTRGEILGIGGLIGSGRTEIAEGICGLRATTNGQILIHGKQQAIGTYADAVKAGLVYLS 337

Query: 104 QELN---LMNHLSAAQNIFIGREPRKA--MGLF--IDEDELNRQAAAIFARMRLDMDP-S 155
           ++     L   LS A+NI +         +GL   + E +L R  A    R+ + M    
Sbjct: 338 EDRKGSGLFLDLSIAKNISVLNLDALTGHLGLIDTVGEGDLARDFAQ---RLNIRMGSIG 394

Query: 156 TPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVY 215
            PV  L+   QQ V IAK L+   +V++MDEPT  ++    +E+  ++R+L   G+GI+ 
Sbjct: 395 APVSSLSGGNQQKVAIAKQLAIQPKVILMDEPTRGIDVGAKSEIHALLRELAQSGIGIIV 454

Query: 216 ISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           IS ++ EL  + DRV V+R+G+    + M + + + +I +  G
Sbjct: 455 ISSELPELLGLCDRVIVIREGEVAGELGMDDMTEERVIRLASG 497


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: 718
Number of extensions: 29
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: 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 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:

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 2024 update 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