GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Williamsia sterculiae CPCC 203464

Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_076475776.1 BW971_RS01220 amino acid permease

Query= TCDB::Q46065
         (463 letters)



>NCBI__GCF_900156495.1:WP_076475776.1
          Length = 480

 Score =  365 bits (938), Expect = e-105
 Identities = 189/436 (43%), Positives = 269/436 (61%), Gaps = 7/436 (1%)

Query: 8   LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67
           LGT L+ RH+TM+ +   IGAGLF+G+   I  AGPAVL++Y++AG +VVLVM+MLGEMA
Sbjct: 30  LGTSLKPRHITMISIAGVIGAGLFVGSANAIEKAGPAVLISYLLAGTLVVLVMRMLGEMA 89

Query: 68  AARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEPWIPS 127
            A P +GSFS Y + A G WAGFS+GWLYW+  ++V+  E T AA+I+    G   WI +
Sbjct: 90  TANPDTGSFSVYSDRALGRWAGFSVGWLYWWFWVLVIPVEATAAASILSDLIGGAQWIWA 149

Query: 128 LVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNFI 187
           L   V   V NL++V  +GEFE+WFA IKV  I+AF+++G   IFG  PGS   G SN  
Sbjct: 150 LAVTVLLTVTNLISVGNYGEFEFWFALIKVVAIVAFIVVGALAIFGVFPGSDVSGISNLW 209

Query: 188 GDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFYL 247
              GF+PNG   V AG+L   F+F G EIVTIAAAES  P   IS AV +VIWRIS+FY+
Sbjct: 210 KPDGFLPNGFGAVIAGMLVTMFSFMGTEIVTIAAAESPNPEAGISKAVNSVIWRISLFYI 269

Query: 248 GSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIYA 307
           GS+ V+  L+PY+ ++      +  +  +L    IP     M+ +I+ A+ S  N+ +Y 
Sbjct: 270 GSIFVVVALLPYDKLD------DGSYQSVLEAIGIPHAKQIMDVVILTAVASCLNSALYT 323

Query: 308 TSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNAV 367
            SR++FS+  R+DAPRV  KL+ + VP  AVL SM   F++V   Y  P  +  +LL   
Sbjct: 324 ASRMLFSLGERRDAPRVVRKLTGNGVPWVAVLASMVIGFLAVVGNYVLPDKIFAYLLATS 383

Query: 368 GGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAAS 427
           G   + V+  I  SQL L ++++A    S VRMW  P+L  + +V +  ++ LM  D  +
Sbjct: 384 GAVALFVYLAIATSQLVLGRKMRATGGRSAVRMWLFPYLTGVVIVFIIAVLILMAFD-PN 442

Query: 428 RSQVYSVAIVYGFLVL 443
           + Q    +I+   +++
Sbjct: 443 QQQAIGFSIISAVIIV 458


Lambda     K      H
   0.327    0.140    0.428 

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: 618
Number of extensions: 32
Number of successful extensions: 2
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: 463
Length of database: 480
Length adjustment: 33
Effective length of query: 430
Effective length of database: 447
Effective search space:   192210
Effective search space used:   192210
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