GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Williamsia sterculiae CPCC 203464

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_076477443.1 BW971_RS04965 PLP-dependent aminotransferase family protein

Query= BRENDA::A0A060PQX5
         (417 letters)



>NCBI__GCF_900156495.1:WP_076477443.1
          Length = 389

 Score =  266 bits (680), Expect = 8e-76
 Identities = 149/394 (37%), Positives = 235/394 (59%), Gaps = 20/394 (5%)

Query: 23  SKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQY 82
           S+    ++ S +R+LL++ E  DV+S+AGGLPA +  P + IAE    V+ +  A ALQY
Sbjct: 9   SRALSSIRGSAIRDLLRVTERPDVLSMAGGLPATDLIPSDRIAEAASRVISE--ASALQY 66

Query: 83  GTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPT 142
             + G  PLR  +A+      +       ++IT GSQQAL L  +  ++PGD V+V+ P 
Sbjct: 67  TVSAGVRPLREVVADRDGTHPE------RVLITHGSQQALFLSAQALLDPGDTVIVDDPV 120

Query: 143 YLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVT 202
           Y+ ALQ F+    E V +P+  EG  VD LE  L +    G + ++V+T+  F NPAGVT
Sbjct: 121 YVGALQVFQSVRAEIVALPITAEGTDVDRLERLLSD----GVRPRIVHTVSNFHNPAGVT 176

Query: 203 MSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAP 262
            S + R+RL ELA+++ F I+ED+PYG+LR++G  + PI       RV+ LG+ SKILAP
Sbjct: 177 ASARTRRRLAELAADHGFWIIEDDPYGQLRFAGRSMDPIPG----DRVIRLGSASKILAP 232

Query: 263 GFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYV-EGGHLDNHIPNIIEFYKPR 321
             R+GW+ A P ++  +E+ +Q  DLC + F+Q++    + +   +  H+ ++   Y  R
Sbjct: 233 ALRVGWLQASPDVVELVELLRQGADLCGSTFAQLMTADLLGDSDFMTAHVSDLRREYARR 292

Query: 322 RDAMLKALEEFMPE--GVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFF 379
             A+  AL   +    GV + +PEGGMF W+ LP G+DT ++L+ AV  GVA+VPG AF 
Sbjct: 293 AAALTGALRTDLGAVCGVEFIEPEGGMFCWLRLP-GLDTAILLDHAVRAGVAFVPGAAFA 351

Query: 380 AHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413
               + + +RL+F  +  +++ E ++RLA  + +
Sbjct: 352 VDAGLGDRLRLSFATLSPDQLTEAVRRLATAVHD 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: 336
Number of extensions: 17
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