Aligments for a candidate for HSERO_RS03640 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for HSERO_RS03640 in Klebsiella michiganensis M5al

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS27035 BWI76_RS27035 xylose ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS27035 BWI76_RS27035 xylose ABC
           transporter ATP-binding protein
          Length = 513

 Score =  389 bits (999), Expect = e-112
 Identities = 223/509 (43%), Positives = 323/509 (63%), Gaps = 28/509 (5%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGV--HAPDQGEI 63
           LL+M+ I K+FGA  A+ ++ L +  GE+ +L GENG+GKSTLMKVL G+  H   +GEI
Sbjct: 4   LLEMKNITKTFGAVKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63

Query: 64  LLDG---RPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM 120
           +  G   +P  +RD   +   GI +I+QELA+  +++V  N+F+G+E+ +R GL+D+  M
Sbjct: 64  IFSGETLQPGHIRD---TERKGIAIIHQELALVKHLTVLENIFLGAEI-SRHGLLDYETM 119

Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
             R + +L Q+          G L + +QQ VEIA+AL  + R++I+DEPTA+L+E+ET 
Sbjct: 120 TLRCEKLLAQVNLAISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETA 179

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
            L N++R L++ G+A IYISH++ EV A++D + V+RDG  +G    D +  + I+ MMV
Sbjct: 180 ILLNIIRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMV 239

Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGG--------KIRPASFDVRAGEVLGFAG 292
           GR L+  Y  +  +  D      +++V  L           ++   SF +R GE+LG AG
Sbjct: 240 GRELTALYPSEAHSCGDE-----ILRVENLTAWHPVNRHIKRVNDVSFSLRRGEILGIAG 294

Query: 293 LVGAGRTELARLLFGADP-RSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQ 351
           LVGAGRTE  + LFG  P R  G I ++G+PV I   + A+  GIA VPEDRK  G+   
Sbjct: 295 LVGAGRTEAVQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPV 354

Query: 352 MAVAANATMNVASRHTRLGLVRSRSLGG---VARAAIQRLNVKVAHPETPVGKLSGGNQQ 408
           MAV  N T+   ++ T  G + S    G     + +IQRL +K + PE  +G+LSGGNQQ
Sbjct: 355 MAVGKNITLAALNQFT--GPLSSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQ 412

Query: 409 KVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGIC 468
           K +LAR L + P++LILDEPTRG+DI AK EIY+L+++L  QG+AV+VISSELPEV+G+ 
Sbjct: 413 KAILARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLS 472

Query: 469 DRVLVMREGMITGELAGAAITQENIMRLA 497
           DRVLVM EG +   L    +TQE +M  A
Sbjct: 473 DRVLVMHEGKLKANLINQGLTQEQVMEAA 501



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 65/237 (27%), Positives = 116/237 (48%), Gaps = 11/237 (4%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSG--GDILLEGRPVHIDQPRAAMRAGI 336
           S  + AGEV+   G  G+G++ L ++L G  P     G+I+  G  +     R   R GI
Sbjct: 24  SLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFSGETLQPGHIRDTERKGI 83

Query: 337 AYVPEDRKGQGLFLQMAVAANATMNVA-SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHP 395
           A + ++     L   + V  N  +    SRH   GL+   ++       + ++N+ ++ P
Sbjct: 84  AIIHQEL---ALVKHLTVLENIFLGAEISRH---GLLDYETMTLRCEKLLAQVNLAIS-P 136

Query: 396 ETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVV 455
           +T VG L  G QQ V +A+ L    ++LILDEPT  +     + +  ++  L + G+A +
Sbjct: 137 DTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAILLNIIRDLQNHGIACI 196

Query: 456 VISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPA-SHS 511
            IS +L EV  I D + V+R+G   G      +++++I+ +     +    P+ +HS
Sbjct: 197 YISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVGRELTALYPSEAHS 253


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: 619
Number of extensions: 25
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 521
Length of database: 513
Length adjustment: 35
Effective length of query: 486
Effective length of database: 478
Effective search space:   232308
Effective search space used:   232308
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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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 preprint on GapMind for carbon sources, or view the source code.

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