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

GapMind for catabolism of small carbon sources

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

Align Maltose phosphorylase (EC 2.4.1.8); Trehalose phosphorylase (EC 2.4.1.64) (characterized)
to candidate WP_035135982.1 Q763_RS15685 glycoside hydrolase family 65 protein

Query= reanno::Pedo557:CA265_RS24655
         (772 letters)



>NCBI__GCF_000769915.1:WP_035135982.1
          Length = 769

 Score =  920 bits (2377), Expect = 0.0
 Identities = 440/767 (57%), Positives = 558/767 (72%), Gaps = 2/767 (0%)

Query: 2   KNYIKADEWNIIEEGFDPHLNKISESIFSLGNGRMGQRANFEETYTGETLPGNYVAGVYY 61
           ++YI  D W+IIEEGF+    K SES+FS+GNG MGQRANFEE Y+G T  G+Y+AGVYY
Sbjct: 3   QDYIVPDNWSIIEEGFEADRVKSSESLFSIGNGAMGQRANFEEHYSGPTFQGSYIAGVYY 62

Query: 62  PDKTRVGWWKNGYPEYFAKVLNAANWIGIEVKLDGEILDLATA-EVSDFKRVLNMHAGYL 120
           PDKT+VGWWKNGYPEYFAKVLNA NWIGIEV+++GE LDL T  E+ ++KR LNM  G+ 
Sbjct: 63  PDKTKVGWWKNGYPEYFAKVLNAPNWIGIEVQVNGEALDLNTCKEIKNYKRELNMKEGWY 122

Query: 121 ERTFTAKLKSGKTLKVKSTRFCSIADDEVGAIRYSITPLNFDGRLTLMPFIDGDVKNQDS 180
            R+FTA L++G  + V   RF S+  DE+G I+Y +TP+N   ++   P++D  VKN+D+
Sbjct: 123 NRSFTAVLQNGTEVAVNVRRFLSLVSDELGVIKYEVTPVNQSAQIVYKPYVDAGVKNEDA 182

Query: 181 NYDEKFWDKVADEISGTEAYIKLRTKKTEFEVCTGSNIELYKNA-EKLAINPEAVRKEKF 239
           N++EKFW+ +  + SG +A++  RT KT F   T  +  L  N  E++ +  + V     
Sbjct: 183 NWEEKFWEPLDVQHSGNDAFVTARTFKTHFTAATYMHNSLLLNGTEEVVVAEDIVATNDK 242

Query: 240 VGQTFSLEVKANEEISLVKIAANLSSENYPKESLLKETKSIIAKASAKGFDTLLKEQTEA 299
           V  ++SL+ K  E  ++VK      S N+ + +L+   K++IA A +KG+D LL+EQ +A
Sbjct: 243 VQFSYSLDAKQGETAAIVKFGGYTVSLNHEEGALIDAAKNVIANAVSKGYDALLEEQKQA 302

Query: 300 WASKWEESDIIIEGDVSAQQAIRFNIFQLFQTYTGKDDRLNIGPKGFTGEKYGGSTYWDT 359
           WA  WE +DI I+GDV AQQ IRFNIFQL QTY GKD RLNIGPKGFTGEKYGGSTYWDT
Sbjct: 303 WAGIWEMADITIDGDVKAQQGIRFNIFQLNQTYLGKDPRLNIGPKGFTGEKYGGSTYWDT 362

Query: 360 EAYCVPFYLATAPQEVSKNLLVYRHKQLGKAIENAAKLGFKDGAALYPMVTMNGEECHNE 419
           EAYC+PFY+AT  Q+V++NLL YRH QLGKAIENA KLGF +GAALYPMVTMNGEECHNE
Sbjct: 363 EAYCIPFYMATKDQQVARNLLTYRHNQLGKAIENAQKLGFTNGAALYPMVTMNGEECHNE 422

Query: 420 WEITFEEIHRNGAIAFAIFNYIRYTGDESYLSDFGLEVLIGIARFWKQRVNWSNDKQQYV 479
           WEITFEEIHRNGAIAFAI+NY R+TGD SY+ + GLEVLIGIARFW QR  +S  K +YV
Sbjct: 423 WEITFEEIHRNGAIAFAIYNYYRFTGDYSYIPEKGLEVLIGIARFWYQRATFSTAKNKYV 482

Query: 480 MLGVTGPNEYENNVNNNWYTNILATWCMKYATEAAEIVKTQQPEKYNSLLKSLNFDQKEF 539
           +LGVTGPNEYENNVNNNWYTN +A WC+ YA E    VK +    ++ ++   N   +E 
Sbjct: 483 ILGVTGPNEYENNVNNNWYTNYIAQWCINYAIENITKVKDEFTADHSRIMGLTNLTAEEI 542

Query: 540 ADWADIIEKMYYPQDEKLGIFLQQDGYLDKEQTLVKDLPASERPINQKWSWDRILRSCFI 599
             W  + + MY+P  E+ G+FLQQDG+LDKE   V DL  S+RPINQKWSWDRILRS +I
Sbjct: 543 QQWQKVADNMYFPYSEEHGVFLQQDGFLDKEMVRVSDLDRSQRPINQKWSWDRILRSPYI 602

Query: 600 KQADVLQGLYFFEEDYDLDTLKRNFDFYEPRTVHESSLSPCVHSILAAKLNDEARAYEFY 659
           KQADVLQG YFFE+ +  + L+++FDFYEP TVHESSLSPCVHSI AA LN   +AY FY
Sbjct: 603 KQADVLQGFYFFEDHFTREDLEKHFDFYEPFTVHESSLSPCVHSIQAAGLNRMEQAYTFY 662

Query: 660 LRTARLDLDDYNNDTEDGLHITSMAGTWMSVVEGFAGMRVREGKLQFNPFLPGKWKSFSF 719
           LRT+RLDLDDYN + ++GLHITSMAGTWMS+VEGF GMRV+ G L F P +P +W+ +SF
Sbjct: 663 LRTSRLDLDDYNKEVKEGLHITSMAGTWMSIVEGFGGMRVKNGNLHFEPRIPEQWEGYSF 722

Query: 720 TIGFRGATLKINITESGISIKNNAAVDLEIGIRNQLYKLAGNTEIEV 766
            I FR   +KI++             +L + +  +  K+  N  + +
Sbjct: 723 KINFRNQIVKISVHSGETRFDLEGDKELTVFVHGKEVKVEPNKAVTI 769


Lambda     K      H
   0.317    0.134    0.401 

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: 1805
Number of extensions: 79
Number of successful extensions: 3
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: 772
Length of database: 769
Length adjustment: 41
Effective length of query: 731
Effective length of database: 728
Effective search space:   532168
Effective search space used:   532168
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 (21.6 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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