GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TAT in Rhodococcus qingshengii djl-6-2

Align tryptophan permease (characterized)
to candidate WP_003943879.1 C1M55_RS01060 amino acid permease

Query= CharProtDB::CH_091156
         (592 letters)



>NCBI__GCF_002893965.1:WP_003943879.1
          Length = 469

 Score =  226 bits (575), Expect = 2e-63
 Identities = 139/400 (34%), Positives = 223/400 (55%), Gaps = 10/400 (2%)

Query: 72  SFDTSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTI 131
           S D   L+ TLK RHL MIAI G IG GLFVGSG AI E GP GV+I +A+AG  +I  +
Sbjct: 3   STDQPALQHTLKKRHLSMIAIAGVIGAGLFVGSGVAIQETGP-GVLISYALAGVVVILVM 61

Query: 132 HGLGEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNS 191
             LGE++   P  G+F++Y  + +     F +  +Y   W  VL +E  A A+ +  W  
Sbjct: 62  RMLGEMSAASPETGSFSSYADKAIGRWAGFSIGWLYAWFWIIVLGIEATAGALIMNRWVP 121

Query: 192 SIDPVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHE 251
            +    W  I   V+   N+  V+ FGE EF F++IK + +  F+ + +V ICG  P  E
Sbjct: 122 GVPQWTWALILMIVLTLTNIISVKSFGEFEFWFASIKVVAIIAFLGMGIVAICGWMPGVE 181

Query: 252 FIG-AKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET-DP-KGLPSAIKQVF 308
             G        G L NG   +L+ ++V  +S  G E+  +A+GE+ +P + + +A+K V 
Sbjct: 182 APGMTNLTGHGGFLPNGTGAMLAAVLVVVFSFFGAEIATIAAGESANPLEAVRAAVKSVV 241

Query: 309 WRILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISV 368
           WRIL F++ S+ +V  L+P+ +      +SV  SP+V  +  + I A  +I++ V+L SV
Sbjct: 242 WRILIFYIGSIAVVVTLLPWDS------ASVALSPYVAVMDSYGIPAAGNIMDVVVLTSV 295

Query: 369 LSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMS 428
           LS  NS ++ +SR + S+A +G  P     I++ G P+  ++ +++ G L   +   S  
Sbjct: 296 LSCLNSGLYTASRMIFSLAGRGDAPKSLSRIEKTGVPMRAVLVSTIVGFLTVGMNYLSPD 355

Query: 429 EVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLD 468
           +VF +L+  +G     VWL I++S +R R  ++A G+ L+
Sbjct: 356 KVFLFLVNSSGAIALFVWLVISVSQLRTRRKLEASGQELE 395


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: 681
Number of extensions: 43
Number of successful extensions: 5
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: 469
Length adjustment: 35
Effective length of query: 557
Effective length of database: 434
Effective search space:   241738
Effective search space used:   241738
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