Alignments for a candidate for HSERO_RS05250 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Klebsiella michiganensis M5al

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Koxy:BWI76_RS14860
          Length = 510

 Score =  457 bits (1177), Expect = e-133
 Identities = 243/495 (49%), Positives = 340/495 (68%), Gaps = 3/495 (0%)

Query: 18  SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77
           SS P++ L  + KR+   LAL+N +F+L AGEVHALMGENGAGKSTLMKILSG  QRDSG
Sbjct: 5   SSPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSG 64

Query: 78  DILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDEL 137
            I +DG+ ++I  PR A+  GI IIHQELN +  ++ A+N+F+G+EP    G+ +D   +
Sbjct: 65  VIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGI-LDRKRM 123

Query: 138 NRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIA 197
           +R+A     R+  D+DP  P+G L++ RQQMVEIA+A+S +++VL++DEPTAAL+ AE  
Sbjct: 124 HREAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETL 183

Query: 198 ELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257
           +L+R+I  ++  GVG+VYISH+M+E+ Q+A+RV+V RDG +I T  +   S   I+ MMV
Sbjct: 184 QLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMV 243

Query: 258 GRALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVAR 317
           GR +    +  P T   DV+LEVR L  G A   VSF +  GE++  +GL+G+GRTEVAR
Sbjct: 244 GRQIVDLYQHEPRTP-GDVLLEVRDL-AGSATGPVSFEVSAGEVVSMSGLVGSGRTEVAR 301

Query: 318 AIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSM 377
            +FGADP   G + + G ++    P  A+A GIG ++EDRK  GL +G  V+ NI +SS+
Sbjct: 302 LLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSL 361

Query: 378 GRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDIL 437
             F   G + ++ IR A    +R+L ++  +VE     LSGGNQQK  +A+WLLRD  +L
Sbjct: 362 DNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLL 421

Query: 438 FFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGEL 497
             DEPTRG+D+GAK EIY+L+D LA  GKAI++ISS+LPE + +S RVLVM  GRI  +L
Sbjct: 422 ILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQL 481

Query: 498 ARADATQEKIMQLAT 512
               AT+E++M  AT
Sbjct: 482 PSCSATEEEVMLHAT 496



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 64/221 (28%), Positives = 108/221 (48%), Gaps = 6/221 (2%)

Query: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102
           FE++AGEV ++ G  G+G++ + ++L G   R  G + L G+  + ++P  A A GIG++
Sbjct: 278 FEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMV 337

Query: 103 HQELN----LMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDP-STP 157
            ++       + H S   NI I        G  +    +         R+RL  +    P
Sbjct: 338 TEDRKTQGLFLGH-SVEHNIDISSLDNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELP 396

Query: 158 VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYIS 217
           V  L+   QQ   +A+ L  DSR+LI+DEPT  ++     E++ +I  L   G  I+ IS
Sbjct: 397 VSALSGGNQQKAALARWLLRDSRLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVIS 456

Query: 218 HKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
             + E   I+DRV VMR G+ +  +P    + + ++    G
Sbjct: 457 SDLPEAIGISDRVLVMRGGRIVHQLPSCSATEEEVMLHATG 497



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 58/230 (25%), Positives = 112/230 (48%), Gaps = 9/230 (3%)

Query: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347
           A+ +V F L  GE+    G  GAG++ + + + G +  ++G I I G    I++P DA  
Sbjct: 24  ALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFIDGQAIDIRTPRDARK 83

Query: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTP 407
           +GI  + ++         M V  N+ L      +  G +D++ +   A+  + ++     
Sbjct: 84  YGIAIIHQE---LNTVPDMTVAENLFLGQEPT-SFAGILDRKRMHREAKEKLNRI---NA 136

Query: 408 SVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQG 465
            ++ QA L  LS G QQ + IA+ +  +  +L  DEPT  +      ++Y+L+  + + G
Sbjct: 137 DIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRLIAQMRQDG 196

Query: 466 KAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515
             +V IS  + EV ++++RV V  +G   G     + +   I+++   R+
Sbjct: 197 VGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVGRQ 246


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: 696
Number of extensions: 35
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: 520
Length of database: 510
Length adjustment: 35
Effective length of query: 485
Effective length of database: 475
Effective search space:   230375
Effective search space used:   230375
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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