Alignments for a candidate for malI in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for malI in Stenotrophomonas chelatiphaga DSM 21508

Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate WP_057507040.1 ABB28_RS02155 MFS transporter

Query= TCDB::Q9A612
         (541 letters)



>NCBI__GCF_001431535.1:WP_057507040.1
          Length = 499

 Score =  541 bits (1394), Expect = e-158
 Identities = 290/496 (58%), Positives = 348/496 (70%), Gaps = 12/496 (2%)

Query: 41  RQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLVQP 100
           + +LSF QIWNMCFGF GIQ GF LQNAN SRIF++LG  +  +  LWIAAP TGLLVQP
Sbjct: 11  KPQLSFWQIWNMCFGFLGIQFGFALQNANASRIFETLGASMEAVPGLWIAAPLTGLLVQP 70

Query: 101 IIGHFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINITMEP 160
           I+G+ SD+TW R+GRRRP+F  GA+LTTLALLVMPNSPTLW+AA  LW++DASIN++MEP
Sbjct: 71  IVGYLSDRTWTRWGRRRPFFMIGAVLTTLALLVMPNSPTLWIAAGTLWVLDASINVSMEP 130

Query: 161 FRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDSVRI 220
           FRAFVGD L   QR TG+AMQSFFIG+GA+ AS LP++L + F VANTA  G+VPD+VR 
Sbjct: 131 FRAFVGDQLAPRQRPTGFAMQSFFIGVGAIVASFLPFILAH-FGVANTAAPGEVPDTVRY 189

Query: 221 AFYTGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAYIALGVG 280
           AFY G   LL A+ WTV +TREYSP +L  F  AE   A         P     + L VG
Sbjct: 190 AFYFGAVVLLAAITWTVLSTREYSPTELAGFADAEPPHAHAVASRGVPPWAQIALWLLVG 249

Query: 281 GVLLGAALALIVWGAGLEKELYVLAGLLFAFG-LAGVAGARFKRIGRTDNGFSEVLADVF 339
            VL     ALI W  G +K LYVLAGL  A+G L GVA     R+    +  + ++ D+ 
Sbjct: 250 IVL----AALITWQRG-DKMLYVLAGLCAAYGILLGVA-----RVLPGTHMLATIVDDLR 299

Query: 340 RMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLFAVY 399
            MP TMR+LA VQFFSWF LFAMWIYTT AVA  HFG+ D  S AYNEGA+WVGVLF  Y
Sbjct: 300 NMPGTMRRLAWVQFFSWFALFAMWIYTTAAVAGTHFGSTDPQSAAYNEGANWVGVLFGAY 359

Query: 400 NGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGFAWSS 459
           NG AALAAL+IPLMV+    R SH V L LG  GL+S + I DP  L + MVGVGFAW+S
Sbjct: 360 NGFAALAALLIPLMVRAIGLRWSHLVNLWLGGAGLVSMMFIDDPRWLLLSMVGVGFAWAS 419

Query: 460 ILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFALVLGA 519
           ILS PY++L+ ++PA KMGVYMGIFN FIV+PQL+AA+ LG  L+ + G Q +  LVLG 
Sbjct: 420 ILSLPYALLSDSVPAAKMGVYMGIFNFFIVIPQLVAASALGFALRAWLGGQPMQVLVLGG 479

Query: 520 LSFALAAAATFLVRDR 535
            S  +A      V  R
Sbjct: 480 CSLLVAGLCVLRVPSR 495


Lambda     K      H
   0.327    0.140    0.437 

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: 909
Number of extensions: 44
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: 541
Length of database: 499
Length adjustment: 35
Effective length of query: 506
Effective length of database: 464
Effective search space:   234784
Effective search space used:   234784
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 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 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