Alignments for a candidate for fruA in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruA in Moritella dasanensis ArB 0140

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_017223098.1 A923_RS0118060 PTS fructose transporter subunit IIBC

Query= TCDB::Q9HY57
         (585 letters)



>NCBI__GCF_000276805.1:WP_017223098.1
          Length = 586

 Score =  652 bits (1681), Expect = 0.0
 Identities = 340/581 (58%), Positives = 439/581 (75%), Gaps = 13/581 (2%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           MK+AIVTACP G  +S++AA LL  A   L W+  +E ++   P   L+ +QIA A+ ++
Sbjct: 1   MKIAIVTACPSGIASSLIAAGLLEKAVTELKWQADIECHSSVAPMTSLTEQQIAAAECIV 60

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDE---------AGL 111
           +     +  +RF+GK VYR+       + +A+L++A   A+  V   E         A  
Sbjct: 61  IAANANVNDSRFIGKKVYRSAVDAVFTEAKAYLEQAIENATELVISHETDSNETNSNASA 120

Query: 112 VAPEAGAAPR--IVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDP 169
           VA     + R  IVA+TACPTGVAHTFMAAEAL+    +LG  ++VET+GSVGA+N L  
Sbjct: 121 VANSNAESRRKTIVAITACPTGVAHTFMAAEALEQEGQRLGHTIKVETRGSVGAKNQLSS 180

Query: 170 ADIAAADVVLLAADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAG-AAS 228
           A+IAAADVV++AADID+D ARF GKK+Y+  TG+ALK+ + T++ A  + QV   G  A+
Sbjct: 181 AEIAAADVVIIAADIDIDLARFDGKKVYKTSTGLALKKTKQTMDNAFNDAQVYRHGKTAA 240

Query: 229 AVVARDEKRGVYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVGD- 287
           +  A  EK G YKHL+TGVS MLP+VVAGGL IALS  FGI+A+K+ G+LAA L T+G  
Sbjct: 241 SGDASSEKTGAYKHLMTGVSHMLPLVVAGGLAIALSFVFGIEAFKEEGTLAAALMTIGGG 300

Query: 288 TAFVLMVPMLAGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISH 347
           +AF LM+P+LAG+IA+SIADRPGLAPG++GG+LA + GAGF+GGIVAGF+AGY A+ I+ 
Sbjct: 301 SAFALMIPVLAGFIAFSIADRPGLAPGLIGGMLASSTGAGFLGGIVAGFLAGYTAKLIAE 360

Query: 348 GLRLPASLEALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLG 407
            ++LP S+EALKPIL+IPLLASL+TGL+M+YVVG PV+  + ALT FL+ MG++NA+LLG
Sbjct: 361 KVQLPQSMEALKPILIIPLLASLITGLVMIYVVGGPVSAAMNALTEFLNNMGSANAVLLG 420

Query: 408 LLLGGMMCVDLGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKF 467
           ++LG MMC DLGGPVNK AY F VGLL+S +YAPMAAVMAAGMVP +GMGLAT LA+RKF
Sbjct: 421 IILGSMMCFDLGGPVNKTAYTFGVGLLASQTYAPMAAVMAAGMVPALGMGLATFLAKRKF 480

Query: 468 AESERQAGKAASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPH 527
             SE++AGKA+ VLGLCFISEGAIPFAA+DP+RVIP+ IAGGALTGALSM FG +L APH
Sbjct: 481 NGSEQEAGKASFVLGLCFISEGAIPFAARDPMRVIPSCIAGGALTGALSMLFGAELMAPH 540

Query: 528 GGLFVMLVPNAINHALAYLLAIVAGSLLTGLLYAVLKRGAE 568
           GGLFV+L+PNAI     YL+AI AG+L+TG+ YAVLK+  E
Sbjct: 541 GGLFVLLIPNAITPVFMYLVAIAAGTLVTGVSYAVLKQSEE 581


Lambda     K      H
   0.321    0.137    0.392 

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: 838
Number of extensions: 40
Number of successful extensions: 9
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: 585
Length of database: 586
Length adjustment: 37
Effective length of query: 548
Effective length of database: 549
Effective search space:   300852
Effective search space used:   300852
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 (21.9 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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 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