Alignments for a candidate for HSERO_RS03640 in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Phyllobacterium brassicacearum STM 196

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_106713128.1 CU102_RS21415 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_003010955.1:WP_106713128.1
          Length = 516

 Score =  408 bits (1048), Expect = e-118
 Identities = 227/500 (45%), Positives = 317/500 (63%), Gaps = 9/500 (1%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           P+L+ RGI K+FG    L+D+ LT+ PGE+HA++GENGAGKSTLMK++SG   P +G + 
Sbjct: 13  PVLEARGIAKAFGPVEVLTDISLTVMPGEVHAIIGENGAGKSTLMKLMSGHLQPTRGTVA 72

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
           +DG PV    P  +   G+ L++QE+ +AP+++VA N+FMG EL+  L + D    R   
Sbjct: 73  IDGEPVHFAGPVDAEHRGLVLVHQEILLAPDLTVAQNIFMGRELKRGLMVNDREMNRQSA 132

Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184
           +AV   LGA    +    RLSIA +Q V+IARAL    R+VI DEPTA+L+  ETE L  
Sbjct: 133 EAV-HSLGADIDPTTQISRLSIARRQLVQIARALQVPHRVVIFDEPTASLTPFETEALLK 191

Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244
           V+R LRD+G+A++YISHR+ EV A+ADR+TVLRDG  +      E+    + ++MVGR +
Sbjct: 192 VIRDLRDKGVAVLYISHRLPEVGAIADRITVLRDGKLIATRNASELQPVDMARLMVGRDM 251

Query: 245 SEFYQHQRIAPADAAQLPTVMQVRAL-AGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303
           S+ Y  +     D     TV++V+     G  R ASF +R GE+LGFAGL+GAGRTEL  
Sbjct: 252 SKLYPERE----DTTSRQTVLEVKNFDVPGYARDASFSLRKGEILGFAGLIGAGRTELFE 307

Query: 304 LLFGADPRSG-GDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV 362
            L G   R+G GDI L G PV     R +M AGI Y+ EDRKG+GL L   +  N T+  
Sbjct: 308 GLVGL--RTGHGDIKLNGAPVKFHGVRDSMAAGIVYLSEDRKGKGLLLAQDLRTNLTLAT 365

Query: 363 ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422
             + T+  L+  +        AI   +++    +   G+LSGGNQQK+LLA+ + + P +
Sbjct: 366 LGKFTKGPLIERKREDKSLDKAISDFDIRARRRDLLAGQLSGGNQQKLLLAKMMLLEPSI 425

Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482
           +I+DEPTRG+DI  K +IY+ +  LA  G +VVVISSE+ E+IGIC R+LVMR   I GE
Sbjct: 426 VIIDEPTRGIDIGTKEQIYKFIASLAKAGKSVVVISSEMQELIGICHRILVMRSSRIVGE 485

Query: 483 LAGAAITQENIMRLATDTNV 502
           + G A+T++ I+  AT   V
Sbjct: 486 VMGEAMTEDEIVVYATGVKV 505



 Score = 98.6 bits (244), Expect = 5e-25
 Identities = 75/259 (28%), Positives = 124/259 (47%), Gaps = 14/259 (5%)

Query: 255 PADAAQLPTVMQVRALAGG-----KIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGAD 309
           P  AA +P V++ R +A        +   S  V  GEV    G  GAG++ L +L+ G  
Sbjct: 6   PTIAATMP-VLEARGIAKAFGPVEVLTDISLTVMPGEVHAIIGENGAGKSTLMKLMSGHL 64

Query: 310 PRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRL 369
             + G + ++G PVH   P  A   G+  V ++     L   + VA N  M    R  + 
Sbjct: 65  QPTRGTVAIDGEPVHFAGPVDAEHRGLVLVHQEIL---LAPDLTVAQNIFMG---RELKR 118

Query: 370 GL-VRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEP 428
           GL V  R +   +  A+  L   +  P T + +LS   +Q V +AR L++  +V+I DEP
Sbjct: 119 GLMVNDREMNRQSAEAVHSLGADI-DPTTQISRLSIARRQLVQIARALQVPHRVVIFDEP 177

Query: 429 TRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAI 488
           T  +  +    + +++  L  +GVAV+ IS  LPEV  I DR+ V+R+G +      + +
Sbjct: 178 TASLTPFETEALLKVIRDLRDKGVAVLYISHRLPEVGAIADRITVLRDGKLIATRNASEL 237

Query: 489 TQENIMRLATDTNVPRTAP 507
              ++ RL    ++ +  P
Sbjct: 238 QPVDMARLMVGRDMSKLYP 256



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 68/245 (27%), Positives = 111/245 (45%), Gaps = 20/245 (8%)

Query: 14  KSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALR 73
           K+F       D   ++R GEI    G  GAG++ L + L G+     G+I L+G PV   
Sbjct: 271 KNFDVPGYARDASFSLRKGEILGFAGLIGAGRTELFEGLVGLRT-GHGDIKLNGAPVKFH 329

Query: 74  DPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM-------RSRTDA 126
               S AAGI  + ++            + +  +LRT L L             R R D 
Sbjct: 330 GVRDSMAAGIVYLSEDRK-------GKGLLLAQDLRTNLTLATLGKFTKGPLIERKREDK 382

Query: 127 VLRQLGAGFGASD-----LAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQ 181
            L +  + F         LAG+LS   QQ++ +A+ ++    IVI+DEPT  +     EQ
Sbjct: 383 SLDKAISDFDIRARRRDLLAGQLSGGNQQKLLLAKMMLLEPSIVIIDEPTRGIDIGTKEQ 442

Query: 182 LFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241
           ++  +  L   G +++ IS  M E+  +  R+ V+R    VGE++ + +  + IV    G
Sbjct: 443 IYKFIASLAKAGKSVVVISSEMQELIGICHRILVMRSSRIVGEVMGEAMTEDEIVVYATG 502

Query: 242 RSLSE 246
             ++E
Sbjct: 503 VKVNE 507


Lambda     K      H
   0.320    0.135    0.378 

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: 739
Number of extensions: 44
Number of successful extensions: 9
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: 521
Length of database: 516
Length adjustment: 35
Effective length of query: 486
Effective length of database: 481
Effective search space:   233766
Effective search space used:   233766
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