GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Rhodococcus qingshengii djl-6-2

Align Valine amino-acid permease; Branched-chain amino-acid permease 3 (characterized)
to candidate WP_003943879.1 C1M55_RS01060 amino acid permease

Query= SwissProt::P41815
         (604 letters)



>NCBI__GCF_002893965.1:WP_003943879.1
          Length = 469

 Score =  185 bits (469), Expect = 4e-51
 Identities = 122/404 (30%), Positives = 209/404 (51%), Gaps = 20/404 (4%)

Query: 86  LKKSMKSRHVVMMSLGTGIGTGLLVANAKGLSLAGPGSLVIGYVMVSFVTYFMVQAAGEM 145
           L+ ++K RH+ M+++   IG GL V +   +   GPG L I Y +   V   +++  GEM
Sbjct: 9   LQHTLKKRHLSMIAIAGVIGAGLFVGSGVAIQETGPGVL-ISYALAGVVVILVMRMLGEM 67

Query: 146 GVTYPTLPGNFNAYNSIFISKSFGFATTWLFCIQWLTVLPLELITSSMTVKYWNDTINAD 205
               P   G+F++Y    I +  GF+  WL+   W+ VL +E    ++ +  W   +   
Sbjct: 68  SAASPET-GSFSSYADKAIGRWAGFSIGWLYAWFWIIVLGIEATAGALIMNRWVPGVPQW 126

Query: 206 VFIVIFYVFLLFIHFFGVKAYGETEFIFNSCKILMVAGFIILSVVINCGGA-GVDGYIGG 264
            + +I  + L   +   VK++GE EF F S K++ +  F+ + +V  CG   GV+     
Sbjct: 127 TWALILMIVLTLTNIISVKSFGEFEFWFASIKVVAIIAFLGMGIVAICGWMPGVEAPGMT 186

Query: 265 KYWRDPGSFAEGSGATRFKGICYILVSAYFSFGGIELFVLSINEQSNPRKSTPVAAKRSV 324
                 G    G+GA     +  +LV   FSF G E+  ++  E +NP ++   A K  V
Sbjct: 187 NLTGHGGFLPNGTGAM----LAAVLV-VVFSFFGAEIATIAAGESANPLEAVRAAVKSVV 241

Query: 325 YRILIIYLLTMILIGFNVPHNNDQLMGSGGSATHASPYVLAASIHKVRVIPHIINAVILI 384
           +RILI Y+ ++ ++   +P ++        ++   SPYV     + +    +I++ V+L 
Sbjct: 242 WRILIFYIGSIAVVVTLLPWDS--------ASVALSPYVAVMDSYGIPAAGNIMDVVVLT 293

Query: 385 SVISVANSALYAAPRLMCSLAQQGYAPKFLNYIDREGRPLRALVVCSLVG--VVGFVACS 442
           SV+S  NS LY A R++ SLA +G APK L+ I++ G P+RA++V ++VG   VG    S
Sbjct: 294 SVLSCLNSGLYTASRMIFSLAGRGDAPKSLSRIEKTGVPMRAVLVSTIVGFLTVGMNYLS 353

Query: 443 PQEEQAFTWLAAIAGLSELFTWSGIMLSHIRFRKAMKVQGRSLD 486
           P  ++ F +L   +G   LF W  I +S +R R+ ++  G+ L+
Sbjct: 354 P--DKVFLFLVNSSGAIALFVWLVISVSQLRTRRKLEASGQELE 395


Lambda     K      H
   0.324    0.138    0.420 

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: 583
Number of extensions: 34
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: 604
Length of database: 469
Length adjustment: 35
Effective length of query: 569
Effective length of database: 434
Effective search space:   246946
Effective search space used:   246946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 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