GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Williamsia sterculiae CPCC 203464

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_076477443.1 BW971_RS04965 PLP-dependent aminotransferase family protein

Query= SwissProt::H3ZPL1
         (417 letters)



>NCBI__GCF_900156495.1:WP_076477443.1
          Length = 389

 Score =  265 bits (676), Expect = 2e-75
 Identities = 148/388 (38%), Positives = 231/388 (59%), Gaps = 20/388 (5%)

Query: 29  MKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQYGTTKGF 88
           ++ S IR+LL++ E  DV+S+AGGLPA +  P + I E    V+ +  A ALQY  + G 
Sbjct: 15  IRGSAIRDLLRVTERPDVLSMAGGLPATDLIPSDRIAEAASRVISE--ASALQYTVSAGV 72

Query: 89  TPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPTYLAALQ 148
            PLR  +A+      +       ++ T GSQQAL L  +  ++PGD ++V+ P Y+ ALQ
Sbjct: 73  RPLREVVADRDGTHPE------RVLITHGSQQALFLSAQALLDPGDTVIVDDPVYVGALQ 126

Query: 149 AFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVTMNEKRR 208
            F+    E V +P+  EG +VD LE  L +    G + +IV+T+  F NPAGVT + + R
Sbjct: 127 VFQSVRAEIVALPITAEGTDVDRLERLLSD----GVRPRIVHTVSNFHNPAGVTASARTR 182

Query: 209 KRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAPGFRIGW 268
           +RL ELA+ + F I+ED+PYG+LR++G  + PI       RVI LG+ SKILAP  R+GW
Sbjct: 183 RRLAELAADHGFWIIEDDPYGQLRFAGRSMDPIPG----DRVIRLGSASKILAPALRVGW 238

Query: 269 IAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYV-EGGYLDKHIPKIIEFYKPRRDAMLK 327
           + A P  +  +E+ +Q  DLC +TF+Q++    + +  ++  H+  +   Y  R  A+  
Sbjct: 239 LQASPDVVELVELLRQGADLCGSTFAQLMTADLLGDSDFMTAHVSDLRREYARRAAALTG 298

Query: 328 ALEEFMPD--GVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVK 385
           AL   +    GV++ +PEGGMF W  LP G+DT ++L+ AV  GVA+VPG AF     + 
Sbjct: 299 ALRTDLGAVCGVEFIEPEGGMFCWLRLP-GLDTAILLDHAVRAGVAFVPGAAFAVDAGLG 357

Query: 386 NTMRLNFTYVPEEKIREGIKRLAETIKE 413
           + +RL+F  +  +++ E ++RLA  + +
Sbjct: 358 DRLRLSFATLSPDQLTEAVRRLATAVHD 385


Lambda     K      H
   0.318    0.137    0.398 

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: 326
Number of extensions: 14
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: 417
Length of database: 389
Length adjustment: 31
Effective length of query: 386
Effective length of database: 358
Effective search space:   138188
Effective search space used:   138188
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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