Alignments for a candidate for HSERO_RS03640 in Cronobacter condimenti 1330

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Cronobacter condimenti 1330

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_007667715.1 BN137_RS14410 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000319285.1:WP_007667715.1
          Length = 503

 Score =  381 bits (979), Expect = e-110
 Identities = 211/497 (42%), Positives = 309/497 (62%), Gaps = 7/497 (1%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           TPLL ++GI K+F    AL ++ L + PG + AL+GENGAGKSTL+KV++G++ PD GEI
Sbjct: 5   TPLLSLKGICKTFPGVRALENVQLELWPGRVTALIGENGAGKSTLVKVMTGIYQPDGGEI 64

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRL-GLIDHAAMRS 122
           L    P+ L +P A+   GI  I+QE  +   ++V  N+F G  L   L   +D  AM  
Sbjct: 65  LYKAIPITLPNPEAAHKVGITAIHQETVLFDELTVTENIFTGHYLVKGLFKKLDWPAMHR 124

Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182
           +   +L +L        +   LSIA++  V IARAL   +++VI+DEPTAALS+ E  + 
Sbjct: 125 QARDILNRLEVNIDPHAVLKTLSIAQRHMVAIARALSFDAQVVILDEPTAALSQHEILEF 184

Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242
           + +V RL+ EG AI++ISH+  E++ LAD  T+LRDG FV      +I  ER+V MMVGR
Sbjct: 185 YQIVERLKHEGKAILFISHKFDEIFELADHYTILRDGVFVSAGDITDITEERMVAMMVGR 244

Query: 243 SLSEFYQHQRIAPADAAQLPTVMQVRALAGG-KIRPASFDVRAGEVLGFAGLVGAGRTEL 301
           ++++ Y      P D     TV++VR L    +     F +R GE+LGF GLVGAGRTEL
Sbjct: 245 AITQTYPKVVCEPGD-----TVLEVRDLCHPTEFAHIDFSLRKGEILGFYGLVGAGRTEL 299

Query: 302 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 361
            + L G    S G+I+L G+ +   QP  A+ AGI  VPE+R+ QG  +++ +A N ++ 
Sbjct: 300 MQALCGVTRPSSGEIILNGKHMAFHQPADAIEAGIVCVPEERQKQGAIIELPIAQNISLP 359

Query: 362 VASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPK 421
             SR    G++       +A    +RL VK +    PV  LSGGNQQKV++A+WL   P+
Sbjct: 360 QLSRLNPNGILHDDREWALADEYARRLQVKASGWRQPVETLSGGNQQKVVIAKWLATRPE 419

Query: 422 VLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITG 481
           V+ILDEPT+G+DI +K+ ++Q +  L  QG+AV+++SSELPEV+G+ DR++VM EG++  
Sbjct: 420 VIILDEPTKGIDIGSKAAVHQFMSELVGQGLAVIMVSSELPEVMGMADRIIVMHEGLMVA 479

Query: 482 ELAGAAITQENIMRLAT 498
           E A    T E+I+  A+
Sbjct: 480 EYAAGKATAESIVSAAS 496



 Score = 93.6 bits (231), Expect = 2e-23
 Identities = 68/224 (30%), Positives = 105/224 (46%), Gaps = 15/224 (6%)

Query: 28  TIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIY 87
           ++R GEI    G  GAG++ LM+ L GV  P  GEI+L+G+ +A   P  +  AGI  + 
Sbjct: 279 SLRKGEILGFYGLVGAGRTELMQALCGVTRPSSGEIILNGKHMAFHQPADAIEAGIVCVP 338

Query: 88  QE---------LAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQLGA-GFGA 137
           +E         L +A NIS+     +        G++      +  D   R+L     G 
Sbjct: 339 EERQKQGAIIELPIAQNISLPQLSRLNPN-----GILHDDREWALADEYARRLQVKASGW 393

Query: 138 SDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAII 197
                 LS   QQ+V IA+ L  R  ++I+DEPT  +       +   +  L  +GLA+I
Sbjct: 394 RQPVETLSGGNQQKVVIAKWLATRPEVIILDEPTKGIDIGSKAAVHQFMSELVGQGLAVI 453

Query: 198 YISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241
            +S  + EV  +ADR+ V+ +G  V E    +  +E IV    G
Sbjct: 454 MVSSELPEVMGMADRIIVMHEGLMVAEYAAGKATAESIVSAASG 497



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 64/227 (28%), Positives = 110/227 (48%), Gaps = 12/227 (5%)

Query: 285 GEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRK 344
           G V    G  GAG++ L +++ G     GG+IL +  P+ +  P AA + GI  + ++  
Sbjct: 33  GRVTALIGENGAGKSTLVKVMTGIYQPDGGEILYKAIPITLPNPEAAHKVGITAIHQETV 92

Query: 345 GQGLFLQMAVAANATMNVASRHTRL-GLVRSRSLGGVARAA---IQRLNVKVAHPETPVG 400
              LF ++ V    T N+ + H  + GL +      + R A   + RL V +  P   + 
Sbjct: 93  ---LFDELTV----TENIFTGHYLVKGLFKKLDWPAMHRQARDILNRLEVNI-DPHAVLK 144

Query: 401 KLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSE 460
            LS   +  V +AR L    +V+ILDEPT  +  +   E YQ+V RL  +G A++ IS +
Sbjct: 145 TLSIAQRHMVAIARALSFDAQVVILDEPTAALSQHEILEFYQIVERLKHEGKAILFISHK 204

Query: 461 LPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAP 507
             E+  + D   ++R+G+         IT+E ++ +     + +T P
Sbjct: 205 FDEIFELADHYTILRDGVFVSAGDITDITEERMVAMMVGRAITQTYP 251


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: 632
Number of extensions: 21
Number of successful extensions: 7
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: 503
Length adjustment: 35
Effective length of query: 486
Effective length of database: 468
Effective search space:   227448
Effective search space used:   227448
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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Protein sequences (fasta format)
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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