GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Phyllobacterium brassicacearum STM 196

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_106709787.1 CU102_RS04475 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_003010955.1:WP_106709787.1
          Length = 514

 Score =  394 bits (1013), Expect = e-114
 Identities = 229/516 (44%), Positives = 326/516 (63%), Gaps = 30/516 (5%)

Query: 10  KAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGG 69
           + P+L++RN+ K F  V+AL  V      GEVHAL GENGAGKSTLM I++G    D G 
Sbjct: 2   REPVLSIRNVTKHFGAVKALTNVNFALERGEVHALCGENGAGKSTLMNIIAGVLQPDEG- 60

Query: 70  ECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVAR-GDMV 128
           E  +DG+ V+I  P +A+ LG+ +++QE++L P+ SVAENI++    ++R L+     + 
Sbjct: 61  EIVLDGKTVRIGSPAAAQSLGLGLVHQEIALCPDASVAENIFMASISRQRSLLMNYRKLE 120

Query: 129 RACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDR 188
           R     ++RL A       V  L I+ +QLVEIA+A+  + R+L+ DEPT  L+  E   
Sbjct: 121 REAQAVMSRL-APIDVRRKVGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTEAEARI 179

Query: 189 LFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248
           LF +IR L+  G++I+YISHRMAEI EL DRVTVLRDG +V T   A L+   +V+ MVG
Sbjct: 180 LFEIIRDLKANGISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVVRRMVG 239

Query: 249 RDLSGFYT-KTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307
           R+++  Y  K       +EV+ SVR + D  R +    DL  GE+LG+ GL+G+GRTE+A
Sbjct: 240 REITQLYPPKQPAGERPQEVVFSVRGLGDNERFRDVDIDLTRGEILGIGGLIGSGRTEIA 299

Query: 308 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 367
             + G  A T G++ I     + G           A+ AG+ YL+EDRK  GLFLD S+ 
Sbjct: 300 EGICGLRATTNGQILIHGKQQAIGTYA-------DAVKAGLVYLSEDRKGSGLFLDLSIA 352

Query: 368 ENINLI--------VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGN 419
           +NI+++        +   D +G G L R  A+R        L IR+      V +LSGGN
Sbjct: 353 KNISVLNLDALTGHLGLIDTVGEGDLARDFAQR--------LNIRMGSIGAPVSSLSGGN 404

Query: 420 QQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVG 479
           QQKV +++ L IQP+V+++DEPTRG+D+GAKSEI+ L+  LAQSG+ I++ISSELPE++G
Sbjct: 405 QQKVAIAKQLAIQPKVILMDEPTRGIDVGAKSEIHALLRELAQSGIGIIVISSELPELLG 464

Query: 480 LCDRVLVMREGTLAGEVRPAGSAAETQERIIALATG 515
           LCDRV+V+REG +AGE+   G    T+ER+I LA+G
Sbjct: 465 LCDRVIVIREGEVAGEL---GMDDMTEERVIRLASG 497


Lambda     K      H
   0.320    0.136    0.382 

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: 681
Number of extensions: 37
Number of successful extensions: 8
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: 540
Length of database: 514
Length adjustment: 35
Effective length of query: 505
Effective length of database: 479
Effective search space:   241895
Effective search space used:   241895
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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