Alignments for a candidate for malI in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for malI in Shewanella amazonensis SB2B

Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate 6937501 Sama_1657 major facilitator transporter (RefSeq)

Query= TCDB::Q9A612
         (541 letters)



>FitnessBrowser__SB2B:6937501
          Length = 518

 Score =  567 bits (1460), Expect = e-166
 Identities = 292/497 (58%), Positives = 362/497 (72%), Gaps = 10/497 (2%)

Query: 44  LSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLVQPIIG 103
           LSF QI+NMCFGF GIQ GF LQNAN SRIFQ+LG  ++ + ILWIA P TGLLVQPI+G
Sbjct: 14  LSFWQIFNMCFGFLGIQFGFALQNANVSRIFQTLGASIDDIPILWIAGPLTGLLVQPIVG 73

Query: 104 HFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINITMEPFRA 163
           + SD TW RFGRRRPYF  GA+LTTLAL +MP+SP LWVAA  LWIMDASINI MEPFRA
Sbjct: 74  YLSDNTWNRFGRRRPYFLIGAVLTTLALFIMPHSPYLWVAAGMLWIMDASINIAMEPFRA 133

Query: 164 FVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDSVRIAFY 223
           FVGD LP+ QRA G+AMQSFFIG+GAV ASALP++L+N+  V+N AP GQ+ D+VR +FY
Sbjct: 134 FVGDKLPESQRAKGFAMQSFFIGIGAVVASALPYLLSNFAGVSNIAPEGQIADTVRYSFY 193

Query: 224 TGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAYIALGVGGVL 283
            GG  LL AV WT+ ++REYSPE+L+ F+  E+  +G   H    P   AY    +    
Sbjct: 194 LGGVVLLAAVGWTIISSREYSPEELSRFKGHEQ--SGFERHHGRTP--EAYRKGALVWST 249

Query: 284 LGAALALIVWGAGLEKELYVLAGLLFAFG-----LAGVAGARFKRIGRTDNGFSEVLADV 338
           LG A+    + A L+K+LY+L   +FAFG      A    A  KR G+    F EV+ D+
Sbjct: 250 LGLAITAATFAADLDKQLYLLGLGVFAFGPLQWYCAQRLSAAGKRSGKLGMVF-EVVDDL 308

Query: 339 FRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLFAV 398
           F MP  M++LA+VQFFSWF LFAMWIYTT AV + H+ + D  SKAYN+GADWVGVLFA 
Sbjct: 309 FHMPHAMKRLALVQFFSWFALFAMWIYTTAAVTSYHYHSSDVLSKAYNDGADWVGVLFAS 368

Query: 399 YNGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGFAWS 458
           YNG AALAA+VIPL   +   + +H + L LG +GL+SF +I DP LLWI M+GVGFAW+
Sbjct: 369 YNGFAALAAMVIPLQCMLLGLKGAHIMNLCLGGIGLMSFYLIADPALLWIPMIGVGFAWA 428

Query: 459 SILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFALVLG 518
           SILS PY+IL+ +LP  K+GVYMGIFN FIV+PQL+AAT+LG +LK+ FGN+ I+AL+LG
Sbjct: 429 SILSVPYAILSTSLPGNKLGVYMGIFNFFIVIPQLVAATVLGFILKSLFGNEPIYALILG 488

Query: 519 ALSFALAAAATFLVRDR 535
             +  LAA +   V  R
Sbjct: 489 GSAMILAALSVLFVPAR 505


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: 808
Number of extensions: 35
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: 518
Length adjustment: 35
Effective length of query: 506
Effective length of database: 483
Effective search space:   244398
Effective search space used:   244398
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