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_004141766.1 Mesci_2580 binding-protein-dependent transport system inner membrane protein

Query= TCDB::Q52813
         (400 letters)



>NCBI__GCF_000185905.1:YP_004141766.1
          Length = 387

 Score =  205 bits (522), Expect = 2e-57
 Identities = 130/383 (33%), Positives = 202/383 (52%), Gaps = 10/383 (2%)

Query: 20  SAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSL 79
           S + + K R+   Q+L +  +   V         NLA     SGF FL    G+++  SL
Sbjct: 3   SLLRNQKVRNALLQVLYVGSIAAMVLAGIVIARRNLADQGITSGFDFLFKSTGWDVNFSL 62

Query: 80  ITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVF 139
           +  +++  Y    L+GI+NTL +   G+  ATI+G ++G+ R S N L   L   YV++F
Sbjct: 63  LPATANDPYWWYFLIGIINTLFLGSVGLILATIVGTIVGLARTSSNDLARLLGRTYVDIF 122

Query: 140 RNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVI 199
           RNIP +L +FFWY  +++ LP PR S    +   L +RGL  P P   +   A   A  +
Sbjct: 123 RNIPLILQVFFWY-AIITHLPTPR-SAHEAWGFLLTSRGLYIPFPNVGSAAFA---AATV 177

Query: 200 AIVASIIIARWAHKRQAAT---GQPFHTVWTAIALIVGLPLLVFVVSGFPLT--FDVPVA 254
           A++A+I++  W  +        GQ     + A A  +    ++  +   P T   D P  
Sbjct: 178 AVIAAIVLPAWLGRTSLLAQPIGQRRTIQFAAAAAALACATIILALGRLPDTPLLDFPAL 237

Query: 255 GKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVT 314
              NL GG  + PEF +L +A++ Y  S+IAEIVRGG + V  GQ EAA +LGL P  V 
Sbjct: 238 QGLNLRGGLRIPPEFATLAIAIAIYGGSYIAEIVRGGFKSVGTGQVEAALSLGLSPWRVF 297

Query: 315 RLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWG 374
            LV +P ALR ++P L +QY+ L K +++ IA+GF+D   +    +N SGQ +E + I  
Sbjct: 298 TLVRLPLALRAMLPILANQYVWLMKATTMGIAVGFTDFFMIVALTINHSGQTLEAIGILM 357

Query: 375 IVYLSLSILTSLFMNWFNAKMAL 397
             +L++++  +   N  N  +AL
Sbjct: 358 AGFLAINLSLAAVFNRINKAIAL 380


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: 434
Number of extensions: 22
Number of successful extensions: 4
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: 387
Length adjustment: 31
Effective length of query: 369
Effective length of database: 356
Effective search space:   131364
Effective search space used:   131364
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