GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Oceanisphaera arctica V1-41

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 WP_104484934.1 UN63_RS01070 amino acid ABC transporter permease

Query= TCDB::Q52813
         (400 letters)



>NCBI__GCF_002936955.1:WP_104484934.1
          Length = 394

 Score =  402 bits (1032), Expect = e-116
 Identities = 202/378 (53%), Positives = 269/378 (71%), Gaps = 1/378 (0%)

Query: 24  DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83
           DP  R++ +QI+ + I+ GF+W++ +NT  NL      +GFGFL   AGF I QSLI +S
Sbjct: 17  DPAKRALLFQIILLAIVAGFIWFIVNNTLTNLETRGITTGFGFLDDPAGFAIAQSLIPYS 76

Query: 84  SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143
              TY R  +VG+LNTLLV+  GI  ATI+GF++G+ RLS NWLIA+L + YVE+FRNIP
Sbjct: 77  EVDTYGRTFVVGLLNTLLVSFLGIIGATILGFILGVARLSPNWLIARLASAYVELFRNIP 136

Query: 144 PLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVA 203
            LL +FFWY  VL  LP PR+S  +  S++LN RGL  P+P+   G   + +AL++AI  
Sbjct: 137 LLLQMFFWYFAVLRTLPSPRDSFNIGDSVFLNVRGLYLPEPLPSAGFHWIWVALLLAIAL 196

Query: 204 SIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGS 263
           +  + R+ H+RQ ATGQ     W ++ LI+ LPLL FV+ G PL +  P    FN   G 
Sbjct: 197 ATWLIRFNHRRQEATGQRLPVGWISLGLILVLPLLTFVMLGAPLDWQYPELRGFNFRDGM 256

Query: 264 VVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQAL 323
            + PEF++L+L+L+ YTA+FIAEIVR GI+ V  GQ+EAA ALG+  S   RLV++PQA+
Sbjct: 257 TIIPEFLALWLSLTIYTAAFIAEIVRSGIQAVSHGQTEAAHALGIKDSLTLRLVIIPQAM 316

Query: 324 RIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLSLSI 382
           R+IIPPLTSQYLNLTKNSSLA AIG+ DLV+V  GT LNQ+GQAIE++ I  +VYL++S+
Sbjct: 317 RVIIPPLTSQYLNLTKNSSLATAIGYPDLVSVFAGTTLNQTGQAIEVIAITMLVYLTISL 376

Query: 383 LTSLFMNWFNAKMALVER 400
             S FMNWFN++MALVER
Sbjct: 377 TVSFFMNWFNSRMALVER 394


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: 553
Number of extensions: 25
Number of successful extensions: 3
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: 394
Length adjustment: 31
Effective length of query: 369
Effective length of database: 363
Effective search space:   133947
Effective search space used:   133947
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