Alignments for a candidate for PS417_11890 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Klebsiella michiganensis M5al

Align Inositol transport system ATP-binding protein (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__Koxy:BWI76_RS14860
          Length = 510

 Score =  431 bits (1108), Expect = e-125
 Identities = 224/495 (45%), Positives = 335/495 (67%), Gaps = 1/495 (0%)

Query: 18  LEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA 77
           +  P LL +  ISK +   +AL +V+  +  G V ALMGENGAGKSTLMKI++G  Q D+
Sbjct: 4   ISSPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDS 63

Query: 78  GEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREM 137
           G I + G+ I   TP  A+K GIA+IHQELN +P M++AEN+++G+E  +   +++ + M
Sbjct: 64  GVIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRM 123

Query: 138 HRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVA 197
           HR   E L R+  ++DP+  +G+LSI  +QMVEIA+AVS ++ +L++DEPT+A++  E  
Sbjct: 124 HREAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETL 183

Query: 198 HLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV 257
            L+ +IA ++  G G+VYI+H+M EV+ +A+ V VFRDG +IG +   ++++  ++ MMV
Sbjct: 184 QLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMV 243

Query: 258 GRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAET 317
           GR++  L+       GD+LL VRDL        VSF++ AGE++ ++GL+GSGRT VA  
Sbjct: 244 GRQIVDLYQHEPRTPGDVLLEVRDLA-GSATGPVSFEVSAGEVVSMSGLVGSGRTEVARL 302

Query: 318 IFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP 377
           +FG  P S G + L G+  + SDP  AI  G  ++TEDRK  GLF   SV  N++++ L 
Sbjct: 303 LFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLD 362

Query: 378 HYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437
           ++   G +++K +RA   +  ++LR++  ++E  +  LSGGNQQKA LARWL+ + RLLI
Sbjct: 363 NFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLI 422

Query: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLD 497
           LDEPTRG+D+GAK EIY LI  LA  G A+++ISS+LPE +G+SDRV+VM  G ++  L 
Sbjct: 423 LDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLP 482

Query: 498 RSEATQEKVMQLASG 512
              AT+E+VM  A+G
Sbjct: 483 SCSATEEEVMLHATG 497



 Score = 97.8 bits (242), Expect = 8e-25
 Identities = 65/244 (26%), Positives = 123/244 (50%), Gaps = 14/244 (5%)

Query: 282 LTLDGVFK---------DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLD 332
           L L+G+ K         +V FDL AGE+  + G  G+G++ + + + G     SG I +D
Sbjct: 10  LRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFID 69

Query: 333 GKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRA 392
           G+A+ I  P  A + G A++ ++       P ++V EN+ +   P     G + +K +  
Sbjct: 70  GQAIDIRTPRDARKYGIAIIHQELNT---VPDMTVAENLFLGQEPTSFA-GILDRKRMHR 125

Query: 393 LCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAE 452
             ++   ++       +  + +LS G QQ   +AR +  N ++L+LDEPT  +      +
Sbjct: 126 EAKEKLNRINADIDP-QAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQ 184

Query: 453 IYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512
           +YRLIA +  +G+ ++ IS  + EV  +++RV V  +G  +GT +    +   ++++  G
Sbjct: 185 LYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVG 244

Query: 513 MTAV 516
              V
Sbjct: 245 RQIV 248



 Score = 73.9 bits (180), Expect = 1e-17
 Identities = 60/231 (25%), Positives = 103/231 (44%), Gaps = 5/231 (2%)

Query: 38  ALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQK 97
           A   V   V  G V+++ G  G+G++ + +++ G      G +RL G+      P AA  
Sbjct: 272 ATGPVSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGSVRLAGRESQPSDPTAAIA 331

Query: 98  AGIAMIHQELN---LMPHMSIAENIWIGR-EQLNSLHMVNHREMHRCTAELLARLRINLD 153
            GI M+ ++     L    S+  NI I   +   +  +V  + +     E + RLR+  +
Sbjct: 332 DGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNFVAGGVVKRKTIRAAVLEQMRRLRLREN 391

Query: 154 PEE-QVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKG 212
             E  V  LS   +Q   +A+ +  DS +LI+DEPT  +       ++ +I  L   GK 
Sbjct: 392 AVELPVSALSGGNQQKAALARWLLRDSRLLILDEPTRGVDIGAKREIYELIDRLARAGKA 451

Query: 213 IVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQ 263
           I+ I+  + E   I+D V V R G  +    + S   + ++    G   SQ
Sbjct: 452 ILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEEEVMLHATGTFTSQ 502


Lambda     K      H
   0.320    0.136    0.381 

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: 631
Number of extensions: 23
Number of successful extensions: 6
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: 517
Length of database: 510
Length adjustment: 35
Effective length of query: 482
Effective length of database: 475
Effective search space:   228950
Effective search space used:   228950
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 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