GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapJ in Synechococcus elongatus PCC 7942

Align AapJ, 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 Synpcc7942_0246 Synpcc7942_0246 extracellular solute-binding protein, family 3

Query= TCDB::Q52812
         (341 letters)



>FitnessBrowser__SynE:Synpcc7942_0246
          Length = 359

 Score =  338 bits (868), Expect = 9e-98
 Identities = 167/326 (51%), Positives = 222/326 (68%), Gaps = 4/326 (1%)

Query: 18  GASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDFCKAVASAVFGDPTK 77
           G    S + L+ V+A+G + CGV   L GF+  D+ GN++G DVD CKA+A+A+F DP  
Sbjct: 36  GNETESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKA 95

Query: 78  VKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFN--FRPVTYYDGQGFMVRKGL 135
           ++Y   ++ ERF AL SGE+D+LSRNTTWT++RD   G N  F P T+YDGQG MVR+  
Sbjct: 96  IEYRSLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNS 155

Query: 136 NVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVNAAYDAGRCDVYT 195
            ++S  +  G +ICV++GTT+ELNLAD  +   +QY  + F N     AAY  GRC+  T
Sbjct: 156 GIQSLQDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVT 215

Query: 196 TDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSWTAYALINAEEFG 255
           +D+S L + R TL + D+H +L  +ISKEPL PA    D  WFD+V W   A I AEEFG
Sbjct: 216 SDRSQLAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFG 275

Query: 256 ITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVGNYGEIFERNIGQ 315
           ITQAN+D+ K S NP+I+RFLG E +  +G  LGL+ND+A   IK VGNYGEI+ERN+GQ
Sbjct: 276 ITQANIDQFKTSKNPEIRRFLGLEGE--LGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQ 333

Query: 316 GSPLKIARGLNALWNKGGIQYAPPVR 341
            SPLK+ RGLN L+  GG+ Y+PP R
Sbjct: 334 QSPLKLNRGLNQLYKNGGLLYSPPFR 359


Lambda     K      H
   0.316    0.134    0.398 

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: 356
Number of extensions: 12
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: 341
Length of database: 359
Length adjustment: 29
Effective length of query: 312
Effective length of database: 330
Effective search space:   102960
Effective search space used:   102960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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