Alignments for a candidate for PS417_11890 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Escherichia coli BW25113

Align Inositol transport system ATP-binding protein (characterized)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

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



>FitnessBrowser__Keio:17628
          Length = 513

 Score =  414 bits (1063), Expect = e-120
 Identities = 235/501 (46%), Positives = 334/501 (66%), Gaps = 12/501 (2%)

Query: 21  PYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA--G 78
           PYLLE+ NI+K F  V A+ +V LR+  G +++L GENG+GKSTLMK++ GIY   +  G
Sbjct: 2   PYLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEG 61

Query: 79  EIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMH 138
           EI   G+ I        ++ GIA+IHQEL L+  +++ ENI++G E  ++  M       
Sbjct: 62  EIIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTL 121

Query: 139 RCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAH 198
           RC  +LLA++ +++ P+ +VG+L + ++Q+VEIAKA++    +LI+DEPT+++TE+E + 
Sbjct: 122 RCQ-KLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSI 180

Query: 199 LFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVG 258
           L  II DL+  G   +YI+HK+NEV AI+D + V RDG +IG + A  M+ D +I+MMVG
Sbjct: 181 LLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVG 240

Query: 259 RELSQLFPLRETPIGDLLLTVRDLT----LDGVFK---DVSFDLHAGEILGIAGLMGSGR 311
           REL+ L+P      GD +L +  LT    ++   K   DVSF L  GEILGIAGL+G+GR
Sbjct: 241 RELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGR 300

Query: 312 TNVAETIFGITPSS-SGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLEN 370
           T   + +FG+ P    G+I +DGK V I +   AI +G A++ EDRK  G+ P ++V +N
Sbjct: 301 TETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360

Query: 371 MEMAVLPHYTGNGFIQQKALRALCE-DMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 429
           + +A L  +TG       A    C  +  ++L+VKT S +  I  LSGGNQQKA+LAR L
Sbjct: 361 ITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCL 420

Query: 430 MTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHE 489
           + NPR+LILDEPTRGID+GAK EIY+LI  L  +G+AVI+ISSELPEVLG+SDRV+VMHE
Sbjct: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480

Query: 490 GELMGTLDRSEATQEKVMQLA 510
           G+L   L     TQE+VM+ A
Sbjct: 481 GKLKANLINHNLTQEQVMEAA 501



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 67/232 (28%), Positives = 120/232 (51%), Gaps = 10/232 (4%)

Query: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSS--GQITLDGKAVRISDPHMAIEK 347
           +V   L+AGEI+ + G  GSG++ + + + GI P  S  G+I   G+ ++ S       K
Sbjct: 22  NVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFAGEEIQASHIRDTERK 81

Query: 348 GFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPS 407
           G A++ ++     L   L+VLEN+ +      T NG +    +   C+ +  ++ +   S
Sbjct: 82  GIAIIHQEL---ALVKELTVLENIFLG--NEITHNGIMDYDLMTLRCQKLLAQVSLSI-S 135

Query: 408 LEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAV 467
            +  +  L  G QQ   +A+ L    RLLILDEPT  +     + +  +I  L   G+A 
Sbjct: 136 PDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLDIIRDLQQHGIAC 195

Query: 468 IMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG--MTAVH 517
           I IS +L EV  +SD + V+ +G+ +GT D +  +++ ++ +  G  +TA++
Sbjct: 196 IYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGRELTALY 247


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: 625
Number of extensions: 33
Number of successful extensions: 10
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: 517
Length of database: 513
Length adjustment: 35
Effective length of query: 482
Effective length of database: 478
Effective search space:   230396
Effective search space used:   230396
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