Alignments for a candidate for fruI in Skermanella stibiiresistens SB22

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Skermanella stibiiresistens SB22

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate WP_037459603.1 N825_RS29020 PTS fructose-like transporter subunit IIB

Query= TCDB::Q1LZ59
         (655 letters)



>NCBI__GCF_000576635.1:WP_037459603.1
          Length = 625

 Score =  356 bits (914), Expect = e-102
 Identities = 218/508 (42%), Positives = 297/508 (58%), Gaps = 50/508 (9%)

Query: 159 AAPVADSHDFLVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADD 218
           AAPVA+    +VA+T+C TGIAHT+MA EAL K A  MG  I+VET G+ G GN LT ++
Sbjct: 141 AAPVAEIPKRIVAITSCPTGIAHTFMAAEALNKAAKAMGHQIRVETQGSVGSGNTLTPEE 200

Query: 219 IKRAKGVIIAADKAVEMDRFNGKPLISRPVAEGIKKPEELINIIL------DGKAEAY-- 270
           I+ A  VIIAAD  V +DRF  K + S    + +K  +++I           G  EA   
Sbjct: 201 IEAADVVIIAADTNVALDRFTHKRVYSTSTGKALKGGKQVITTAFAEAAQPGGGGEAATP 260

Query: 271 -VADNSDLSSEASSSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPK 329
            V  N     E   +E++   +  YKHLM+GVS  +P V+ GG+ IALSF+         
Sbjct: 261 GVGKNLAGEVERLKAERSSQRTGPYKHLMTGVSYTIPVVVAGGLAIALSFMFGIDAAKEP 320

Query: 330 SSLSHLGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLA 389
            SL+        AA+    G AAF  M+PV + +IA+SIA++PGL  G + G +A     
Sbjct: 321 GSLA--------AALMQIGGQAAFALMVPVLSGFIAFSIADRPGLAPGLIGGMLANQ--- 369

Query: 390 FNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSIL 449
                               I +GFLG LA GF+AG +   L+ A   +P++LEG+K +L
Sbjct: 370 --------------------IGAGFLGGLASGFMAGYIAYYLR-AWIKLPQNLEGLKPVL 408

Query: 450 LYPLLGVLVTGFLMLFV-NIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPF 508
           + PLL  +  G LM++V   P+AAI + L  +L  ++  +AV LGL++GGMMA+DMGGP 
Sbjct: 409 IIPLLASVAVGLLMIYVVGTPIAAILSGLTAWLSGMTSANAVFLGLLLGGMMAVDMGGPI 468

Query: 509 NKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLT 568
           NK+AY F    L +        + MA+VMA GM PPL + +AT+L KN+FTQ+E DAG  
Sbjct: 469 NKSAYTFAVGLLASETY-----LPMAAVMAAGMTPPLGLALATMLAKNRFTQDERDAGKA 523

Query: 569 NIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL-- 626
             V+G+SFITEGAIPF A DP R IP  IVGSA+TGAL  L G +L APHGGIFV+ +  
Sbjct: 524 ASVLGISFITEGAIPFAAKDPLRVIPPGIVGSALTGALSMLFGCELRAPHGGIFVLGIPN 583

Query: 627 -TSNPLLYLLYIAVGAVIAGILFGSLRK 653
             ++  LY L I +G V+  +L   L+K
Sbjct: 584 AVTHVGLYALAIVIGTVVTAVLVILLKK 611



 Score = 58.2 bits (139), Expect = 1e-12
 Identities = 36/105 (34%), Positives = 57/105 (54%)

Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228
           +VAVT   +  AHT MA EAL+  A  +G  I+VE  G  G  ++L+  DI+ A+ VI+A
Sbjct: 4   VVAVTGSRSSAAHTAMAAEALEITADMLGYDIRVERLGPEGPMDRLSEGDIRAAEVVILA 63

Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVAD 273
            D+  +  RF+GK +     +E I+    ++   L  +    VA+
Sbjct: 64  TDQPDDQGRFHGKSIHRTTPSEAIRHTARVLRDALGDRELEPVAE 108


Lambda     K      H
   0.320    0.137    0.381 

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: 953
Number of extensions: 58
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 655
Length of database: 625
Length adjustment: 38
Effective length of query: 617
Effective length of database: 587
Effective search space:   362179
Effective search space used:   362179
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: 54 (25.4 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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