Alignments for a candidate for malP in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for malP in Escherichia coli BW25113

Align maltose phosphorylase (EC 2.4.1.8) (characterized)
to candidate 15436 b1316 predicted hydrolase (NCBI)

Query= metacyc::MONOMER-13019
         (754 letters)



>FitnessBrowser__Keio:15436
          Length = 755

 Score =  269 bits (687), Expect = 5e-76
 Identities = 213/756 (28%), Positives = 353/756 (46%), Gaps = 78/756 (10%)

Query: 27  SMTSLGNGYMGMRGDFEEGYSGDSLQGIYLGGVWYPDKTRVGWWKNGYPKYFGKVVNAVN 86
           S+ + GNGY+G+R   EE Y+  + +G+YL G+++    R G  +        ++VN  +
Sbjct: 22  SLMAQGNGYLGLRASHEEDYTRQT-RGMYLAGLYH----RAGKGE------INELVNLPD 70

Query: 87  FIKLPIEINGEPVDLAKDKISDFTLDLDMHQGVLNRSFVVERG-AVRVALNFQRFLSVAQ 145
            + + I INGE   L+ +    +  +LD   G L R+ V          +  +RF+S  Q
Sbjct: 71  VVGMEIAINGEVFSLSHEA---WQRELDFASGELRRNVVWRTSNGSGYTIASRRFVSADQ 127

Query: 146 PELSVQKVTVKNLSDAEVDVTLKPSIDADVMNEEANY-DERFWDVLATDQQADRGSIVAK 204
             L   ++T+  L DA+  V +   IDA   N    + DE    V    Q   +GS   +
Sbjct: 128 LPLIALEITITPL-DADASVLISTGIDATQTNHGRQHLDET--QVRVFGQHLMQGSYTTQ 184

Query: 205 TTPNPFGTPRFTSGMEMRLVTDLKNVAITQPNEKEVTTAYTGKLAPQASAELE------- 257
                          + R    +        + ++  TA   +L    SA+L        
Sbjct: 185 ---------------DGRSDVAISCCCKVSGDVQQCYTAKERRLLQHTSAQLHAGETMTL 229

Query: 258 KRVIVVTSRDYDTQESL----TAAMHQLSDKVAQSSYEDLLNAHTAIWAQRWEKSDVVIK 313
           ++++ +  RD D Q +L    +A++ QL +  AQ SY+ LL A T  W Q W+K  + + 
Sbjct: 230 QKLVWIDWRD-DRQAALDEWGSASLRQL-EMCAQQSYDQLLAASTENWRQWWQKRRITVN 287

Query: 314 GDD-ESQQGIRFNLFQLFSTYYGEDARLNIGPKGFTGEKYGGATYWDTEAFAFPVYLGIT 372
           G +   QQ + + L+ L       D R +I  KG TGE Y G  +WDTE F  P +L  +
Sbjct: 288 GGEAHDQQALDYALYHLRIMTPAHDERSSIAAKGLTGEGYKGHVFWDTEVFLLPFHL-FS 346

Query: 373 DPKVTRNLLMYRYKQLDGAYINAQEQGLKGALFPMVTFDGIE--------------CHNE 418
           DP V R+LL YR+  L GA   A+  G +GALFP  +    E                 +
Sbjct: 347 DPTVARSLLRYRWHNLPGAQEKARRNGWQGALFPWESARSGEEETPEFAAINIRTGLRQK 406

Query: 419 WEITFEEIHRNGDIAFAIYNYTRYTGDDSYVLHEGAKVLTEISRFWADRVHFSKRNNQYM 478
                 E H   DIA+A+  Y + TGD+S++ HEG  +L E ++FW  R    + N++  
Sbjct: 407 VASAQAEHHLVADIAWAVIQYWQTTGDESFIAHEGMALLLETAKFWISRA--VRVNDRLE 464

Query: 479 IHGVTGADEYENNVDNNWDTNMLAQWTLKYTLEILGKVDQDTAKQLDVSDEEKT-KWQDI 537
           IH V G DEY  +V+NN  T+ +A++ ++  L I        A+Q   SD+    + +  
Sbjct: 465 IHDVIGPDEYTEHVNNNAYTSYMARYNVQQALNI--------ARQFGCSDDAFIHRAEMF 516

Query: 538 VDRMYLPYDKDLNIFVQHDGFLDKDIEPVS--SIPADQRPINQNWSWDKILRSPYIKQGD 595
           +  +++P  +   +  Q D F+ K    ++     A ++ I  ++S  ++     +KQ D
Sbjct: 517 LKELWMPEIQPDGVLPQDDSFMAKPAINLAKYKAAAGKQTILLDYSRAEVNEMQILKQAD 576

Query: 596 VLQGIWDFIDDYTPEQKKANFDFYEPLTVHESSLSPAIHSVLAADLHYEDKAVELYSRTA 655
           V+   +   + ++     AN  FYEP T+H+SSLS AIH ++AA      ++ + +    
Sbjct: 577 VVMLNYMLPEQFSAASCLANLQFYEPRTIHDSSLSKAIHGIVAARCGLLTQSYQFWREGT 636

Query: 656 RLDLDNYNNDTTDGLHITSMTGAWIAVVQGFAGMRVRDGQLHYAPFLPKTWTSYTFRQVF 715
            +DL    +   DG+H  +    W+  +QGFAG+ VRDG+LH  P LP+ W   +F   +
Sbjct: 637 EIDLGADPHSCDDGIHAAATGAIWLGAIQGFAGVSVRDGELHLNPALPEQWQQLSFPLFW 696

Query: 716 RDRLIEVSVHADGPHFKLLSGEPLTIDVAGAAAAAA 751
           +    E+ V  D     + +  P+++ + G     A
Sbjct: 697 QG--CELQVTLDAQRIAIRTSAPVSLRLNGQLITVA 730


Lambda     K      H
   0.318    0.135    0.408 

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: 1379
Number of extensions: 71
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 754
Length of database: 755
Length adjustment: 40
Effective length of query: 714
Effective length of database: 715
Effective search space:   510510
Effective search space used:   510510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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