Alignments for a candidate for bglF in Tatumella morbirosei LMG 23360

GapMind for catabolism of small carbon sources

Alignments for a candidate for bglF in Tatumella morbirosei LMG 23360

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_038023671.1 HA49_RS15945 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000757425.2:WP_038023671.1
          Length = 634

 Score =  371 bits (953), Expect = e-107
 Identities = 222/633 (35%), Positives = 348/633 (54%), Gaps = 25/633 (3%)

Query: 3   ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62
           EL+  I+  VGG  NI +L HCATRLR +    ++     +++ PG+I VV+ GGQFQ+V
Sbjct: 5   ELSEGIIREVGGETNIRTLTHCATRLRMEFNQRNRVNPPAIEQLPGVISVVDKGGQFQIV 64

Query: 63  IGNHVADVFLAVNSVAGLDEKAQQAPENDDKG----NLLNRFVYVISGIFTPLIGLMAAT 118
           IGN V  VF A+       +      E++ K     N+++R + VIS  FTP+I  +   
Sbjct: 65  IGNDVQRVFSAIQKKRNASQPDATQSEDEVKDSPHQNIMSRIISVISTTFTPVIPAITGA 124

Query: 119 GILKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIG 178
           G++K +L +       +  S +Y +L   +DA F+F P++L Y A  +F  +P  AM + 
Sbjct: 125 GMIKALLVILTLTGVLSSDSSSYQLLNIIADAAFFFLPVLLAYGASVKFECSPILAMTVA 184

Query: 179 GALVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWL 238
           G L+HP I     +G+      +DFLGI V L +YS SV+PII + WL S +ER    + 
Sbjct: 185 GVLLHPGIAQMMASGKP-----VDFLGIKVLLADYSGSVLPIILTVWLMSWIERFAEKYS 239

Query: 239 PSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQ 298
           PS IK F  P++ L+   P+  ++VGPL  ++++++A+    + Q        +MGG   
Sbjct: 240 PSIIKFFIKPMIVLIFSAPLALVVVGPLGIFLNDMVASAAAVIDQHARWLIPMLMGGLQP 299

Query: 299 IFVMFGLHWGLVPLCINNFTVLGYDTMI-PLLMPAIMAQVGAALGVFLCERDAQKKVVAG 357
             V+ G  W + P+     +  G++ +  P ++ + +AQ  A L V L  +++  + +A 
Sbjct: 300 FLVITGTAWAMTPIATGQLSKNGFEMINGPGMLASNIAQGAATLCVALKTKNSGLRQLAS 359

Query: 358 SAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQ 417
           SA  T+L GITEP++YGV L  K P + A I G       G +    Y+F  P +     
Sbjct: 360 SAGFTALMGITEPSLYGVTLRLKRPLIAAMIGGGCAGIYAGLSGLVRYAFVSPGLAALPA 419

Query: 418 TIPSTGIDFTVWASVIGGVIAIGCAFVGTVMLHF----ITAKRQPAQGAP-QEKTPEVIT 472
            I +  ++     ++I  +IA+   F+ T +L F    ++     A  AP   +TPE   
Sbjct: 420 FIGANPMNIV--HALITCLIALVVTFILTWILGFEDSVLSVPETTATVAPLTSETPE--- 474

Query: 473 PPEQGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLH 532
             ++  + SP+ GE+ PL  V D  F+ GLLG G+AI P  G +R+P  G+I     + H
Sbjct: 475 -DDELRVFSPLQGEVKPLSAVNDDVFSGGLLGNGVAIEPQEGILRAPFNGKIQMFLPSRH 533

Query: 533 AIGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLT 592
           A+GI  + G+E+LIH+GIDTV L GK+F + +  GD+V+ GD L+ FD  AIR AG+DL 
Sbjct: 534 AVGILHESGLELLIHIGIDTVNLQGKYFDSDLQPGDEVSRGDVLVRFDTEAIRAAGYDLI 593

Query: 593 TPVLISNSDDFT--DVLPHGTAQISAGEPLLSI 623
           TPV++ NSDD++  D L  G  +   GE L+++
Sbjct: 594 TPVVVVNSDDYSLQDCLETGAVEF--GEVLMTL 624


Lambda     K      H
   0.324    0.141    0.427 

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: 1114
Number of extensions: 65
Number of successful extensions: 5
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: 625
Length of database: 634
Length adjustment: 38
Effective length of query: 587
Effective length of database: 596
Effective search space:   349852
Effective search space used:   349852
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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