Alignments for a candidate for treP in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for treP in Flavobacterium beibuense F44-8

Align Alpha,alpha-trehalose phosphorylase; TPase; EC 2.4.1.64 (characterized)
to candidate WP_035135982.1 Q763_RS15685 glycoside hydrolase family 65 protein

Query= SwissProt::Q8L164
         (774 letters)



>NCBI__GCF_000769915.1:WP_035135982.1
          Length = 769

 Score =  467 bits (1201), Expect = e-135
 Identities = 272/770 (35%), Positives = 427/770 (55%), Gaps = 29/770 (3%)

Query: 13  EDWVIRETQFSIDTNYRNETIFTLANGYIGMRGTFEERYSGPKNTSFNGTYINGFY--EI 70
           ++W I E  F  D    +E++F++ NG +G R  FEE YSGP   +F G+YI G Y  + 
Sbjct: 9   DNWSIIEEGFEADRVKSSESLFSIGNGAMGQRANFEEHYSGP---TFQGSYIAGVYYPDK 65

Query: 71  HDIVYPEGGYG--FAKIGQTMLNVADSKIIKLYVDGEEFDLLQGK-ILFYERVLDMKKGF 127
             + + + GY   FAK+    LN  +   I++ V+GE  DL   K I  Y+R L+MK+G+
Sbjct: 66  TKVGWWKNGYPEYFAKV----LNAPNWIGIEVQVNGEALDLNTCKEIKNYKRELNMKEGW 121

Query: 128 VERKVKWESPTGKILEVKIKRIVSLNRQHLAAISFTMQPVNFTGKIRFVSAIDGNVSNIN 187
             R        G  + V ++R +SL    L  I + + PVN + +I +   +D  V N  
Sbjct: 122 YNRSFTAVLQNGTEVAVNVRRFLSLVSDELGVIKYEVTPVNQSAQIVYKPYVDAGVKN-- 179

Query: 188 DSEDVRVGSNLKGKVLKTIDKSVEGLKGWIVQKTQKSNFSYACAIDNVLVADSKYEVSNS 247
             ED    +N + K  + +D    G   ++  +T K++F+ A  + N L+ +   EV  +
Sbjct: 180 --ED----ANWEEKFWEPLDVQHSGNDAFVTARTFKTHFTAATYMHNSLLLNGTEEVVVA 233

Query: 248 LE----EDGVKVIVDLEAEKGTSYTLNKFISYYTSKDFDENKLVALALEEIEKAKNDGFE 303
            +     D V+    L+A++G +  + KF  Y  S + +E  L+  A   I  A + G++
Sbjct: 234 EDIVATNDKVQFSYSLDAKQGETAAIVKFGGYTVSLNHEEGALIDAAKNVIANAVSKGYD 293

Query: 304 TIEKEQEEFLNSFWKDADVIIEGDKALQQGIRFNEFHLLQS-VGRDGKTNIAAKGLTGGG 362
            + +EQ++     W+ AD+ I+GD   QQGIRFN F L Q+ +G+D + NI  KG TG  
Sbjct: 294 ALLEEQKQAWAGIWEMADITIDGDVKAQQGIRFNIFQLNQTYLGKDPRLNIGPKGFTGEK 353

Query: 363 YEGHYFWDSDIYIMPFFLYTKPE-IAKALVMYRYNLLDAARSRAKELG--HKGALYPWRT 419
           Y G  +WD++ Y +PF++ TK + +A+ L+ YR+N L  A   A++LG  +  ALYP  T
Sbjct: 354 YGGSTYWDTEAYCIPFYMATKDQQVARNLLTYRHNQLGKAIENAQKLGFTNGAALYPMVT 413

Query: 420 IDGPECSAYFPAGTAQYHINADIVYALKRYVEATNDVDFLYDYGCEILFETARFWEDLGA 479
           ++G EC   +     + H N  I +A+  Y   T D  ++ + G E+L   ARFW     
Sbjct: 414 MNGEECHNEWEITFEEIHRNGAIAFAIYNYYRFTGDYSYIPEKGLEVLIGIARFWYQRAT 473

Query: 480 YIPLKGNKFCINCVTGPDEYTALVDNNAYTNYMAKMNLEYAYDIANKMKKEVPQKYQKVA 539
           +   K NK+ I  VTGP+EY   V+NN YTNY+A+  + YA +   K+K E    + ++ 
Sbjct: 474 FSTAK-NKYVILGVTGPNEYENNVNNNWYTNYIAQWCINYAIENITKVKDEFTADHSRIM 532

Query: 540 SKLNLKDEEIVAWKKAADNMYLPYSKELDIIPQDDSFLYKERITVDEIPEDQFPLLLHWH 599
              NL  EEI  W+K ADNMY PYS+E  +  Q D FL KE + V ++   Q P+   W 
Sbjct: 533 GLTNLTAEEIQQWQKVADNMYFPYSEEHGVFLQQDGFLDKEMVRVSDLDRSQRPINQKWS 592

Query: 600 YLNIYRYQICKQPDVLLLMFLQREKFTKDELKKNYDYYEPITTHDSSLSPAIFSILANEI 659
           +  I R    KQ DVL   +   + FT+++L+K++D+YEP T H+SSLSP + SI A  +
Sbjct: 593 WDRILRSPYIKQADVLQGFYFFEDHFTREDLEKHFDFYEPFTVHESSLSPCVHSIQAAGL 652

Query: 660 GYTDKAYKYFMMTARMDLDDYNDNVKDGIHAASMAGTWSAVVNGFGGMRVYTNELHFEPR 719
              ++AY +++ T+R+DLDDYN  VK+G+H  SMAGTW ++V GFGGMRV    LHFEPR
Sbjct: 653 NRMEQAYTFYLRTSRLDLDDYNKEVKEGLHITSMAGTWMSIVEGFGGMRVKNGNLHFEPR 712

Query: 720 LPKEWNLLSFNVRYKGRKINVKLTKENVVFALLEGEPIEIYYFDKKILLE 769
           +P++W   SF + ++ + + + +      F L   + + ++   K++ +E
Sbjct: 713 IPEQWEGYSFKINFRNQIVKISVHSGETRFDLEGDKELTVFVHGKEVKVE 762


Lambda     K      H
   0.318    0.137    0.407 

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: 1630
Number of extensions: 75
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 774
Length of database: 769
Length adjustment: 41
Effective length of query: 733
Effective length of database: 728
Effective search space:   533624
Effective search space used:   533624
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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 2024 update 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