GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Mesorhizobium ciceri WSM1271

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate YP_004143815.1 Mesci_4656 polar amino acid ABC transporter inner membrane subunit

Query= TCDB::Q52813
         (400 letters)



>NCBI__GCF_000185905.1:YP_004143815.1
          Length = 395

 Score =  514 bits (1323), Expect = e-150
 Identities = 253/381 (66%), Positives = 305/381 (80%)

Query: 20  SAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSL 79
           S + DPK R IF+Q+L +V+LV  VWW+AHN   NL R   ASGFGFL+GRAGF+I +S 
Sbjct: 15  SFINDPKIRGIFFQVLVVVLLVAGVWWIAHNVIDNLTRLRIASGFGFLKGRAGFDISESA 74

Query: 80  ITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVF 139
           I +SSDSTY RA+LVG+LNT++VA+ GI TATIIGF+IGIGRLS+NWLI K+CTVYVEVF
Sbjct: 75  IAYSSDSTYGRAILVGLLNTVIVAIVGIITATIIGFVIGIGRLSKNWLIRKICTVYVEVF 134

Query: 140 RNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVI 199
           RNIPPLLVIFFWY GVL+VLP PR+S+ LPF  +LN RG  FP+ ++  G   + +AL++
Sbjct: 135 RNIPPLLVIFFWYSGVLAVLPAPRDSINLPFGSFLNQRGFYFPRAVWGDGSWLIFVALLV 194

Query: 200 AIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNL 259
            I  +  +AR A +RQ ATGQ F   WT+ ALIVGLPLL + +SGFPL+FD P    FNL
Sbjct: 195 GIAMAWFVARKARQRQMATGQQFPVFWTSAALIVGLPLLAYALSGFPLSFDYPKQSTFNL 254

Query: 260 TGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVV 319
           TGG  V PEF+SL+LALS YTA+FIAEIVR GIRGV  GQ+EAAGALGL   S+ RLVVV
Sbjct: 255 TGGFQVRPEFLSLYLALSCYTAAFIAEIVRAGIRGVSAGQTEAAGALGLRSGSILRLVVV 314

Query: 320 PQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLS 379
           PQA+RI+IPPLTSQYLNLTKNSSLAIAIG+ DL A  GT+LNQ+GQA+E V I  ++YL+
Sbjct: 315 PQAMRIVIPPLTSQYLNLTKNSSLAIAIGYPDLTATAGTVLNQTGQAVEGVVIMMVIYLA 374

Query: 380 LSILTSLFMNWFNAKMALVER 400
           +S+LTSL MNWFNAKMALVER
Sbjct: 375 ISLLTSLVMNWFNAKMALVER 395


Lambda     K      H
   0.327    0.141    0.432 

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: 646
Number of extensions: 31
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: 400
Length of database: 395
Length adjustment: 31
Effective length of query: 369
Effective length of database: 364
Effective search space:   134316
Effective search space used:   134316
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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