Alignments for a candidate for H281DRAFT_01113 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Escherichia coli BW25113

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Keio:1937256
          Length = 500

 Score =  306 bits (784), Expect = 1e-87
 Identities = 182/501 (36%), Positives = 279/501 (55%), Gaps = 12/501 (2%)

Query: 13  QPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQL 72
           Q  L   G+ K F GV AL  V  S +RG+I  LLGENG GKSTLIK ++G    D G +
Sbjct: 7   QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTI 66

Query: 73  VIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRV 132
            +EG   +  +   A   GI TVYQ+++LLPNMSVA+N+ +        GR  + F    
Sbjct: 67  WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFI--------GREPKRFGLLR 118

Query: 133 LAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQ 192
                 RA E +   G S      + +  +A +Q+VAI RAI   AK +I+DEPT SL  
Sbjct: 119 RKEMEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDT 178

Query: 193 KEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQIS 252
           +EV+ L  ++  LR +GV+++FV+H LD+ Y +   + VLR+G  +      E  + ++ 
Sbjct: 179 QEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELV 238

Query: 253 ELMTGRHLSNERYRESAH---AQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSG 309
           ++M GR L     + +     +   V   + + + G  +    ++  GEI+G+ GLL SG
Sbjct: 239 KMMLGRELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSG 298

Query: 310 RNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDN 369
           R E A  + G+ PA SG  L+ G+   LR+P  A    IG+ PEDR  +G+     +R+N
Sbjct: 299 RTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVREN 358

Query: 370 VITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWL 429
           +I A+  + R     I R   Q +AE+ +++L I TP  ++P++ LSGGNQQ+VL+ RWL
Sbjct: 359 IILAL-QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWL 417

Query: 430 AIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKK 489
              P+ LIL  PT G+DVG+   I R+++ L   G+ +++IS +L EL+   DR+++M+ 
Sbjct: 418 LTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRD 477

Query: 490 GHVSAEYRADELSEADLYHAL 510
               AE    ELS   + +A+
Sbjct: 478 RKQVAEIPLAELSVPAIMNAI 498



 Score = 87.0 bits (214), Expect = 1e-21
 Identities = 62/223 (27%), Positives = 111/223 (49%), Gaps = 7/223 (3%)

Query: 289 DVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRI 348
           +V F L  GEI+ + G   +G++ L +AL GV  A  G + L+GQ I+ +  + A++  I
Sbjct: 27  NVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGI 86

Query: 349 GYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGV 408
           G V ++     L  +  + DN+    I     RFG + R   +  A + +     +   V
Sbjct: 87  GTVYQE---VNLLPNMSVADNLF---IGREPKRFGLLRRKEMEKRATELMASYGFSLD-V 139

Query: 409 DKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGII 468
            +P+   S   QQ V I R + +  +VLIL  PT  +D    ++++ +M++L  RG+ +I
Sbjct: 140 REPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLI 199

Query: 469 LISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALL 511
            ++  L ++ Q  DRI +++ G         EL + +L   +L
Sbjct: 200 FVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMML 242


Lambda     K      H
   0.319    0.135    0.376 

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: 565
Number of extensions: 23
Number of successful extensions: 8
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: 515
Length of database: 500
Length adjustment: 34
Effective length of query: 481
Effective length of database: 466
Effective search space:   224146
Effective search space used:   224146
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 (21.7 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