Alignments for a candidate for malI in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for malI in Shewanella loihica PV-4

Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate 5209403 Shew_1874 major facilitator transporter (RefSeq)

Query= TCDB::Q9A612
         (541 letters)



>FitnessBrowser__PV4:5209403
          Length = 524

 Score =  582 bits (1500), Expect = e-170
 Identities = 303/512 (59%), Positives = 368/512 (71%), Gaps = 15/512 (2%)

Query: 36  GGSMARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATG 95
           G +  +  LSF QI+NMCFGF GIQ GF LQNAN SRIFQ+LG  ++ + ILWIAAP TG
Sbjct: 18  GTTTVKPALSFWQIFNMCFGFLGIQFGFALQNANVSRIFQTLGAAIDDIPILWIAAPLTG 77

Query: 96  LLVQPIIGHFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASIN 155
           LLVQPIIG+ SD TWGR GRRRPYF  GAI TTLA+ +MP+SP LWVAA  LWIMDASIN
Sbjct: 78  LLVQPIIGYMSDNTWGRLGRRRPYFLIGAIFTTLAIFIMPHSPVLWVAAGMLWIMDASIN 137

Query: 156 ITMEPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVP 215
           I MEPFRAFVGDNLP +QR  GYAMQSFFIG+GAV ASALP++LTN+FDVANTAP G++ 
Sbjct: 138 IAMEPFRAFVGDNLPTKQRPLGYAMQSFFIGVGAVVASALPYLLTNYFDVANTAPEGEIA 197

Query: 216 DSVRIAFYTGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAYI 275
           DSVR AFY GGA LLLAV WTVFTT+EYSPE+L  FE+   E   + LH +      +++
Sbjct: 198 DSVRYAFYFGGAVLLLAVSWTVFTTKEYSPEELARFEQENGE--QVTLHHD-----RSWL 250

Query: 276 ALGVGGV---LLGAALALIVWGAGLEKELYVLAGLLFAFG-LAGVAGARFKRI---GRTD 328
           A   G +   L+GA L  +++   L+K+LY+LA  +FAFG L        K I    R  
Sbjct: 251 AYQKGAMLWSLVGAILTAVIFLQSLDKQLYLLALGIFAFGPLQWFCANTLKHIKGEERHQ 310

Query: 329 NGFSEVLAD-VFRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNE 387
            G    + D +F MPK MRQLAVVQFFSWF LF+MWIYTT AV   H+G  D  SKAYN+
Sbjct: 311 QGMVFSVVDALFHMPKAMRQLAVVQFFSWFALFSMWIYTTAAVTDHHYGTQDVLSKAYND 370

Query: 388 GADWVGVLFAVYNGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLW 447
           GADWVG+LFA YNG AA+AA+ IPL+      +V+H + L  G +GL+SF  I+DP LLW
Sbjct: 371 GADWVGMLFASYNGFAAVAAIFIPLLAMAVGLKVTHLINLCCGGIGLISFYFIQDPNLLW 430

Query: 448 IGMVGVGFAWSSILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFF 507
           + M+GVG AW+SILS PY++L+ ALPA KMGVYMGIFN FIV+PQLLAA++LG++L  FF
Sbjct: 431 LPMIGVGIAWASILSIPYALLSNALPAAKMGVYMGIFNFFIVIPQLLAASVLGVLLNAFF 490

Query: 508 GNQSIFALVLGALSFALAAAATFLVRDRVAGA 539
             + IFAL+LG     LA  +   V    + A
Sbjct: 491 DGKPIFALILGGSFMILAGISVLFVSSEASKA 522


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: 870
Number of extensions: 33
Number of successful extensions: 2
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: 524
Length adjustment: 35
Effective length of query: 506
Effective length of database: 489
Effective search space:   247434
Effective search space used:   247434
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 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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 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