Alignments for a candidate for fruA in Belnapia rosea CPCC 100156

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruA in Belnapia rosea CPCC 100156

Align PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized)
to candidate WP_090662798.1 BLR02_RS10220 PTS fructose transporter subunit EIIBC

Query= SwissProt::P23355
         (580 letters)



>NCBI__GCF_900101615.1:WP_090662798.1
          Length = 566

 Score =  727 bits (1877), Expect = 0.0
 Identities = 391/575 (68%), Positives = 457/575 (79%), Gaps = 15/575 (2%)

Query: 1   MSSSIVVIAAGERSTEAVLAAEALRRAATAAGRSVTIEIRSDQGVLGALPTELTNGAAHV 60
           MS  I V+ AG    +A+LAAEALR+AA   GR + +E+R+++GV+  LP   T  A  +
Sbjct: 1   MSRIIAVVEAGGNPVQAMLAAEALRQAARRGGRDLAVEVRTERGVISPLPASPTADA--L 58

Query: 61  LIVGDADADTARFGDAQLLHLSLGAVLDDPAAAVSQL-AATTAPASTSATTDASGAGGKR 119
           L+VG+A A     G  Q +H  +  VL DPA  +++L     APA+         A G+R
Sbjct: 59  LLVGEAAAPAGLAG-MQAIHAGIAEVLADPAGVLARLDGGVPAPAA---------ARGQR 108

Query: 120 IVAITSCPTGIAHTFMAAEGLQQAAKKLGYQMRVETQGSVGAQDALTDEEIRAADVVIIA 179
           IVAITSCPTGIAHTFMAAEGL+ AAK LG+Q+RVETQGSVGAQ+ALT EEI AAD+V+IA
Sbjct: 109 IVAITSCPTGIAHTFMAAEGLEGAAKALGHQIRVETQGSVGAQNALTPEEIAAADLVLIA 168

Query: 180 ADREVDLARFGGKRLFKSGTKPAINDGPALIQKALAEAGVHGGAAPVAGANATSDAKGNA 239
           AD +VDL+RFG KR+F SGTK AINDG AL+ +ALAEA   GGA   A A+A   A   +
Sbjct: 169 ADTQVDLSRFGAKRVFLSGTKAAINDGQALVTRALAEATEQGGAQ--ATASAAPAAGKRS 226

Query: 240 RTGAYKHLMTGVSFMLPFVTAGGLLIALAFALGGIYAGDDAHQGTLAWSLFQIGAKAGFT 299
            +G YKHLMTGVSFMLPF  AGGLLIALAFALGGIYA DDAH+ TLA +LFQIG KA   
Sbjct: 227 LSGPYKHLMTGVSFMLPFTVAGGLLIALAFALGGIYAFDDAHRDTLAGALFQIGGKAALA 286

Query: 300 LMVPALAGYIAYSIADRPGIAPGMIGGLVAANLNAGFLGGIIAGFIAGYGVAALNRYIKL 359
           LMVPAL GYIAYSIADRPGIAPGMIGG++AA LNAGFLGGI+AGF+AGY V  LNR ++L
Sbjct: 287 LMVPALGGYIAYSIADRPGIAPGMIGGMIAAQLNAGFLGGIVAGFVAGYSVTWLNRALRL 346

Query: 360 PRNLEGLKPVLILPVLGTLLVGLAMMYVFGQPVADLLAWLTAWLRGMQGSSALLLGLLLG 419
           PR LEGLKPVLILPVLG L+ GLA++YV G PVA  LAWLT +LRGMQGS A+LLGLLLG
Sbjct: 347 PRTLEGLKPVLILPVLGALITGLALIYVAGGPVAVALAWLTEFLRGMQGSGAILLGLLLG 406

Query: 420 GMMAFDMGGPVNKAAYAFSTGLIASQVYTPMAAAMVAGMTPPLGIALATWVFRNRFTVEE 479
           GMMAFDMGGPVNKAAYAFSTGL+ASQVY+PMAAAMVAGM PPLG+ALA ++FR+RFT EE
Sbjct: 407 GMMAFDMGGPVNKAAYAFSTGLLASQVYSPMAAAMVAGMVPPLGLALAAFLFRDRFTPEE 466

Query: 480 RGSATAAGVLGLAFVTEGAIPYAARDPLRTIPALVIGSAVAGAISMTAGAELKAPHGGIF 539
           R +A AAGVLGLAF++EGAIP+AA+DPLR IPALV GSAVAGAISM  GAEL+ PHGG+F
Sbjct: 467 REAAPAAGVLGLAFISEGAIPFAAKDPLRVIPALVAGSAVAGAISMAVGAELRVPHGGVF 526

Query: 540 VLLIPNAVTHLLNYVLALVVGVVVTAVALRLLKKP 574
           VL IPNAV+ L  YV+AL+ G VVTA+ALRLLK+P
Sbjct: 527 VLPIPNAVSQLGGYVVALLAGTVVTALALRLLKRP 561


Lambda     K      H
   0.320    0.135    0.386 

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: 850
Number of extensions: 27
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: 580
Length of database: 566
Length adjustment: 36
Effective length of query: 544
Effective length of database: 530
Effective search space:   288320
Effective search space used:   288320
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 (21.8 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 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