Alignments for a candidate for potE in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for potE in Shewanella amazonensis SB2B

Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate 6939241 Sama_3335 putrescine transporter (RefSeq)

Query= SwissProt::P0AAF1
         (439 letters)



>FitnessBrowser__SB2B:6939241
          Length = 438

 Score =  665 bits (1717), Expect = 0.0
 Identities = 327/430 (76%), Positives = 376/430 (87%)

Query: 6   SNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFAKCGMF 65
           +NK+GVVQLTILT+VNMMGSGIIMLPT+LA+VGTISI+SWLVTA GS ALA+AFAKCGMF
Sbjct: 5   NNKIGVVQLTILTIVNMMGSGIIMLPTQLAQVGTISILSWLVTAAGSTALAFAFAKCGMF 64

Query: 66  SRKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLGASLSPVQIG 125
           S+KSGGMGGYAEYAFG+SGNFMANYTY VSLLIANVAIAISAVGYG  L    LSP+   
Sbjct: 65  SKKSGGMGGYAEYAFGRSGNFMANYTYAVSLLIANVAIAISAVGYGAVLFDVELSPIATC 124

Query: 126 LATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVDSWNPHH 185
           LATIGVLW+ TVANFGGARITGQ+SSITVWG+I+PV+G+ +IGWFWF   LY  +WNPH 
Sbjct: 125 LATIGVLWLATVANFGGARITGQVSSITVWGIILPVIGVSLIGWFWFDFDLYKSAWNPHD 184

Query: 186 APFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYIVSTNVI 245
            PFF A+G SIAMTLWAFLGLESACAN++ VENPE+NVPIAV+GGTLGAA+IYIVSTNVI
Sbjct: 185 LPFFEALGGSIAMTLWAFLGLESACANSEAVENPEKNVPIAVMGGTLGAALIYIVSTNVI 244

Query: 246 AGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQVFKSSSD 305
           AGIVPN ELA S APFGLAFAQMF P +G ++MA  ++SC GSLLGWQFTIAQVFK+S+D
Sbjct: 245 AGIVPNGELALSNAPFGLAFAQMFNPTIGAIVMACAIISCTGSLLGWQFTIAQVFKASAD 304

Query: 306 EGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVTNIIPYI 365
           EG+FPK+FS+VTK DAPV GML IV IQS L+LMTISPSLN QF  LVNLAVVTNIIPYI
Sbjct: 305 EGFFPKLFSKVTKADAPVLGMLAIVSIQSVLSLMTISPSLNKQFEALVNLAVVTNIIPYI 364

Query: 366 LSMAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTFLGWTLY 425
           LSMAAL ++QK   +P SKA++AN +A +GA+YSFYALYSSGE A++ GSI TF GWTLY
Sbjct: 365 LSMAALGVMQKQMKIPVSKARIANCMAVMGALYSFYALYSSGETAVMLGSIATFFGWTLY 424

Query: 426 GLVSPRFELK 435
           G++S + EL+
Sbjct: 425 GVISKKNELR 434


Lambda     K      H
   0.323    0.136    0.411 

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: 829
Number of extensions: 28
Number of successful extensions: 1
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: 439
Length of database: 438
Length adjustment: 32
Effective length of query: 407
Effective length of database: 406
Effective search space:   165242
Effective search space used:   165242
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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