GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potE in Sinorhizobium meliloti 1021

Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate SMa0678 SMa0678 putrescine transporter

Query= SwissProt::P0AAF1
         (439 letters)



>FitnessBrowser__Smeli:SMa0678
          Length = 452

 Score =  497 bits (1280), Expect = e-145
 Identities = 244/433 (56%), Positives = 326/433 (75%), Gaps = 1/433 (0%)

Query: 1   MSQAKSNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFA 60
           M  A   KM +VQLT +  VNMMGSGIIMLP  +A+VG IS++SWLVTAVGSMA+A+ FA
Sbjct: 10  MEAASKKKMNLVQLTFIVAVNMMGSGIIMLPANMAQVGAISLLSWLVTAVGSMAIAYGFA 69

Query: 61  KCGMFSRKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLG-ASL 119
           + G+F+++ GGM  YAE A+GK G F+    Y +SL + NVAI ISAVGY        + 
Sbjct: 70  QAGLFNQRPGGMSAYAEDAYGKPGYFLVFLLYFLSLAVGNVAIGISAVGYLAGFFPWLTS 129

Query: 120 SPVQIGLATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVD 179
           +P+   ++ I +LW+ TVANFGG R+TG+I SITVWGVI+PV  LCIIGW WFS  ++  
Sbjct: 130 TPIATCVSLIILLWLTTVANFGGPRVTGRIGSITVWGVILPVGLLCIIGWAWFSSEVFAA 189

Query: 180 SWNPHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYI 239
           +WNP+       +GSSI++TLWAFLG+ESA  N+D VENP+R+VP+A L GTLGAA+IYI
Sbjct: 190 AWNPNGLTLVQGMGSSISLTLWAFLGMESAAQNSDAVENPKRDVPLACLFGTLGAAIIYI 249

Query: 240 VSTNVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQV 299
           +ST VI GIVPN ELA ST PF LAFA MF P +G V+MAL V++C GSLLGWQFTIAQ 
Sbjct: 250 LSTTVIQGIVPNAELAASTGPFALAFATMFNPAIGSVVMALAVLACVGSLLGWQFTIAQT 309

Query: 300 FKSSSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVT 359
            ++++DE  FP +FSRV ++ APV GM+ + ++QS LALMTISP+LN QF  LVNLAVVT
Sbjct: 310 ARAAADERMFPSLFSRVNEMGAPVTGMIVMGVVQSLLALMTISPTLNEQFAALVNLAVVT 369

Query: 360 NIIPYILSMAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTF 419
           N++PYI+S++AL ++ + A V  SK ++ + +A VG +YS +A+Y+SG++A+L G +VT 
Sbjct: 370 NVLPYIISLSALFVMMRAAGVSESKFRLNSSIAIVGMLYSVFAIYASGKDAVLGGMLVTG 429

Query: 420 LGWTLYGLVSPRF 432
           + + +YGL++PRF
Sbjct: 430 IAFIIYGLIAPRF 442


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: 714
Number of extensions: 37
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: 439
Length of database: 452
Length adjustment: 32
Effective length of query: 407
Effective length of database: 420
Effective search space:   170940
Effective search space used:   170940
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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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:

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:

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:

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:

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