Aligments for a candidate for PS417_11890 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for PS417_11890 in Klebsiella michiganensis M5al

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS00275 BWI76_RS00275 ribose ABC
           transporter ATP-binding protein RbsA
          Length = 501

 Score =  479 bits (1233), Expect = e-139
 Identities = 246/491 (50%), Positives = 339/491 (69%), Gaps = 2/491 (0%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86
           LL++  + K FPGV ALS   L V PG V+AL+GENGAGKST+MK++ GIY  DAG L  
Sbjct: 4   LLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGSLLW 63

Query: 87  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146
            GK  TF+ P ++ +AGI +IHQELNL+P ++IAENI++GRE +N F  ID + M+    
Sbjct: 64  LGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123

Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206
           +LL +L +  + ++ VG+LSI ++QMVEIAK +S++S ++IMDEPT A+TD E   LF +
Sbjct: 124 KLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183

Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266
           I +LK+QG+GI+YI+H+M E+F I D+V VFRDG +I  +   S+D D LI MMVGR+L 
Sbjct: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGRKLE 243

Query: 267 QLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGIT 326
             +P  +K  G + + V +L   GV + +SF L  GEILG+AGLMG+GRT + + ++G  
Sbjct: 244 DQYPRLDKAPGAVRLKVDNLCGSGV-ENISFILRQGEILGVAGLMGAGRTELMKVLYGAL 302

Query: 327 PSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYA-G 385
           P   G + LDG+ V    P   +  G   ++EDRK  GL   +SV ENM +  L +++ G
Sbjct: 303 PRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRG 362

Query: 386 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 445
            G ++ K  +    D  +   VKTPS+EQ I  LSGGNQQK  +AR LMT P++LILDEP
Sbjct: 363 GGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422

Query: 446 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 505
           TRG+DVGAK EIY+LI+   +EG+++I++SSE+PEVLGMSDR+MVMHEG L G   R +A
Sbjct: 423 TRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQA 482

Query: 506 TQERVMQLASG 516
           TQE +M  A G
Sbjct: 483 TQEVLMAAAVG 493



 Score = 87.8 bits (216), Expect = 8e-22
 Identities = 59/227 (25%), Positives = 109/227 (48%), Gaps = 6/227 (2%)

Query: 43  LSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQA 102
           + ++   +R G +L + G  GAG++ LMK++ G     +G + L G+ V   +P   L  
Sbjct: 268 VENISFILRQGEILGVAGLMGAGRTELMKVLYGALPRSSGSVTLDGREVVARSPQDGLAN 327

Query: 103 GIAMIHQELN---LMPHMSIAENIWIG--REQLNGFHMIDHREMHRCTAQLLERLRINLD 157
           GI  I ++     L+  MS+ EN+ +   R    G   + H++  +  +  +    +   
Sbjct: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRGGGSLKHKDEQQAVSDFIRLFNVKTP 387

Query: 158 PEEQ-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKG 216
             EQ +G LS   +Q V IA+ +     +LI+DEPT  +       ++ +I   KA+G  
Sbjct: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKAEGLS 447

Query: 217 IIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR 263
           II ++ +M EV  ++D + V  +G   G    +    + L++  VG+
Sbjct: 448 IILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQATQEVLMAAAVGK 494


Lambda     K      H
   0.321    0.137    0.391 

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: 664
Number of extensions: 32
Number of successful extensions: 7
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: 501
Length adjustment: 35
Effective length of query: 486
Effective length of database: 466
Effective search space:   226476
Effective search space used:   226476
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, 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