GapMind for catabolism of small carbon sources

 

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

Align lysine-specific permease (characterized)
to candidate WP_003943879.1 C1M55_RS01060 amino acid permease

Query= CharProtDB::CH_003129
         (489 letters)



>NCBI__GCF_002893965.1:WP_003943879.1
          Length = 469

 Score =  305 bits (782), Expect = 2e-87
 Identities = 162/455 (35%), Positives = 258/455 (56%), Gaps = 13/455 (2%)

Query: 7   TTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLM 66
           +T+ P L+  LK RHL+MIAI G IG GLFV SG  I + GPG  L+SY L G++V  +M
Sbjct: 3   STDQPALQHTLKKRHLSMIAIAGVIGAGLFVGSGVAIQETGPG-VLISYALAGVVVILVM 61

Query: 67  TSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFP 126
             LGE++A  P +GSF++Y    +    GF++GW Y + W + + ++  A  L+M+ W P
Sbjct: 62  RMLGEMSAASPETGSFSSYADKAIGRWAGFSIGWLYAWFWIIVLGIEATAGALIMNRWVP 121

Query: 127 DTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQ 186
             P W W+ + + V+ L N ISV+ FGE E+WF+ IKV  +I F+ +G++ I G   G +
Sbjct: 122 GVPQWTWALILMIVLTLTNIISVKSFGEFEFWFASIKVVAIIAFLGMGIVAICGWMPGVE 181

Query: 187 PAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVF 246
             G +N T        G  AM+   ++V FSF G E+  IAAGES +P + +  AV+ V 
Sbjct: 182 APGMTNLTGHGGFLPNGTGAMLAAVLVVVFSFFGAEIATIAAGESANPLEAVRAAVKSVV 241

Query: 247 WRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILT 306
           WRIL+FY+ +I ++  ++P+        D   +++SP+  V    G+ +A  +M+ V+LT
Sbjct: 242 WRILIFYIGSIAVVVTLLPW--------DSASVALSPYVAVMDSYGIPAAGNIMDVVVLT 293

Query: 307 AVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFG 366
           +VLS  NSG+Y ++RM+++LA  G AP+  +++ + GVP  A+  +T++  L    +   
Sbjct: 294 SVLSCLNSGLYTASRMIFSLAGRGDAPKSLSRIEKTGVPMRAVLVSTIVGFLTVGMNYLS 353

Query: 367 NQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFAFI 426
              V+L+L+N+SG      WL I++S  R RR     G    +L  +  FFP        
Sbjct: 354 PDKVFLFLVNSSGAIALFVWLVISVSQLRTRRKLEASG---QELELKMWFFPYLTYATIA 410

Query: 427 LCLIITLGQ-NYEAFLKDTIDWGGVAATYIGIPLF 460
             + + +G    ++     I   G+AA  +GI L+
Sbjct: 411 AIIALCIGMLTLDSTRSQMIVSLGLAAILVGIGLY 445


Lambda     K      H
   0.327    0.142    0.451 

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: 711
Number of extensions: 53
Number of successful extensions: 3
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: 489
Length of database: 469
Length adjustment: 34
Effective length of query: 455
Effective length of database: 435
Effective search space:   197925
Effective search space used:   197925
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 (21.7 bits)
S2: 51 (24.3 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