GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TAT in Brucella inopinata BO1

Align tryptophan permease (characterized)
to candidate WP_008508798.1 BIBO1_RS14845 amino acid permease

Query= CharProtDB::CH_091156
         (592 letters)



>NCBI__GCF_000182725.1:WP_008508798.1
          Length = 467

 Score =  176 bits (446), Expect = 2e-48
 Identities = 120/390 (30%), Positives = 195/390 (50%), Gaps = 18/390 (4%)

Query: 77  NLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGE 136
           +L R L  RHL +IAIGG+IGTGLF+GSGKA++  GP  +++ +AI G  +   +  LGE
Sbjct: 18  HLARNLSNRHLQLIAIGGTIGTGLFMGSGKAVSLAGP-SILLIYAITGFMLFFVMRALGE 76

Query: 137 ITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPV 196
           I +      +FA++   +L P   F     Y L W      E++A +  V +W   + P 
Sbjct: 77  ILLSNLQYRSFADFAGDYLGPCAQFFTGWTYWLCWIVTAVAEVVAVSGYVSFWFPHLAPW 136

Query: 197 IWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGG-----GPDHE 251
           I       +++ +NL  VR FGE EF F+ IK IT+ G II  + ++  G     G    
Sbjct: 137 IPALGLITILLILNLPTVRNFGEIEFWFALIKIITIIGLIITGIYMLMTGFVLPNGTQAS 196

Query: 252 FIGAKYWHDPGCLANGFPGVLSVLVVASYSLGGIEM--TCLASGETDPKGLPSAIKQVFW 309
              A  W+  G   NG  G ++   ++ ++  GIE+  T  A  E   + LP AI  +  
Sbjct: 197 I--AHLWNHGGFFPNGSLGFIAGFQISVFAFVGIELVGTAAAEAENPMRNLPKAINNIPI 254

Query: 310 RILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVL 369
           RI+ F++ +L ++  + P+   +       ++SPFV    L  I      +N V+L S  
Sbjct: 255 RIVLFYIGALFVIITVTPWNQVD------PNSSPFVAMFSLAGIGIAAHFINFVVLTSAS 308

Query: 370 SVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGL--LAFLVKSGSM 427
           S  NS I+++SR +  +A  GL P  F  +     P+  ++ + +F L  +  L    SM
Sbjct: 309 SSSNSGIYSTSRMVYGLATVGLAPKAFSKLSNRKVPVHALIFSCIFLLSSVVLLYAGQSM 368

Query: 428 SEVFNWLMAIAGLATCIVWLSINLSHIRFR 457
            +VF  +  I+ L    +W  I +S++++R
Sbjct: 369 IQVFTLVTTISALLFIFIWSIILVSYLQYR 398


Lambda     K      H
   0.326    0.141    0.447 

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: 739
Number of extensions: 35
Number of successful extensions: 7
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: 592
Length of database: 467
Length adjustment: 35
Effective length of query: 557
Effective length of database: 432
Effective search space:   240624
Effective search space used:   240624
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 (21.6 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