GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Synechococcus elongatus PCC 7942

Align NatB, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Synpcc7942_1861 Synpcc7942_1861 periplasmic binding protein of ABC transporter for natural amino acids

Query= TCDB::Q8YVY4
         (441 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1861 Synpcc7942_1861
           periplasmic binding protein of ABC transporter for
           natural amino acids
          Length = 421

 Score =  387 bits (993), Expect = e-112
 Identities = 189/382 (49%), Positives = 262/382 (68%), Gaps = 1/382 (0%)

Query: 55  GLKIGSLLPATGDLASIGQQMAAAVPLVVETVNACGGVNGQPVSLVAVDDQTDPKAGAAG 114
           GLK+GSLLP TGDLA  G+ M     L+V+TVNACGGV G PV L+  DD+T P  G A 
Sbjct: 34  GLKLGSLLPLTGDLAQYGRPMQDTAELLVQTVNACGGVQGLPVRLIPADDETKPDRGVAA 93

Query: 115 MTKLATVDKVAGVVGSFASSVSTAAVSIAAQNKVLLISPGSTSPVFTEKAQKGDFNGFWA 174
           MTKLA VD+VAGVVG+ AS+VS AA+++A  N+V++ISP STSP FTE+A++GDF G+W 
Sbjct: 94  MTKLAEVDRVAGVVGAAASNVSDAALTLAVNNRVVMISPSSTSPRFTERARRGDFKGYWF 153

Query: 175 RTVPPDSYQGPALAELANKKGFKRVSTIVINNDYGVGFEKAFVQAFEKLGGTVVNKNNPV 234
           RT P D+ QGPALA+LA  +G++ VS I INNDYG G  ++F+ AFE+ GG V N++ PV
Sbjct: 154 RTAPSDALQGPALAKLALDQGWRSVSVIAINNDYGNGLLRSFIPAFEQAGGVVFNRDQPV 213

Query: 235 RYDPKATTFETEAAAAFAGKPDAVLGVFYVETGSLLLKSAYQQG-VAQGVQIMLTDGMKS 293
            Y P A++F++E    F  +PDAV+ + Y ++G+L+LKSAY++G + Q  Q++LTDG+K+
Sbjct: 214 LYTPDASSFDSEVEQVFRDRPDAVVLIGYPDSGALILKSAYEKGLLGQSTQMLLTDGLKT 273

Query: 294 DEFPAQVGKTADGKFIASGIIGTVPGSDGKGLEALTKLWQSKKGSAPGEFAPQAWDATAL 353
           D+    VG+   G++I   ++G  P S G G EA  K +Q +   +P  F    WDA AL
Sbjct: 274 DQLAELVGRNPQGRYIVQDLVGVAPSSGGPGREAFLKRYQERFQRSPQVFDANTWDAAAL 333

Query: 354 LVLAAQAAKENTGVGIAGKIRDVSSAPGVEVTDVCEGLKLLQEGKDINYQGASGNVDIDA 413
           LVLAA+ +K   G  +   +  +++ PG  V+D+C+ L L++ GK INYQGAS  + +D 
Sbjct: 334 LVLAAEKSKSLEGEKLKDSVAAIANGPGEPVSDICQALALVRAGKPINYQGASSELKLDN 393

Query: 414 NGDVIGVYDVWTVGDDGKIKTI 435
           NGDV G YD W    DGK+K +
Sbjct: 394 NGDVSGRYDFWQFDADGKVKIL 415


Lambda     K      H
   0.312    0.130    0.367 

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: 419
Number of extensions: 12
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: 441
Length of database: 421
Length adjustment: 32
Effective length of query: 409
Effective length of database: 389
Effective search space:   159101
Effective search space used:   159101
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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