GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Phaeobacter inhibens BS107

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate GFF2831 PGA1_c28770 taurine--pyruvate aminotransferase Tpa

Query= curated2:Q8R7C1
         (393 letters)



>FitnessBrowser__Phaeo:GFF2831
          Length = 465

 Score =  201 bits (511), Expect = 4e-56
 Identities = 137/430 (31%), Positives = 214/430 (49%), Gaps = 57/430 (13%)

Query: 17  PIMLVKGEGTRVWDSEGNAYLDFVAG-IAVNSLGHCHPALVEAIKKQAETLIHCSNLYWN 75
           P ++V+G+G RVWD  G  +LD V+G +   ++G+    + +A+  Q   L + +    +
Sbjct: 36  PRIIVEGKGMRVWDQNGKEWLDAVSGGVWTVNVGYGREEIAKAVYDQLMKLCYFAQSAGS 95

Query: 76  EKQIELARMISENSFG-GKVFFANSGAEANEGAIKLARKYASLKYGGKRYKIITAKNSFH 134
                 A  + E   G  +V++ NSG+EANE A K+ R+ A  KYGGK+ KI+     +H
Sbjct: 96  IPGALFAEKLIEKMPGMSRVYYNNSGSEANEKAFKMVRQIAHKKYGGKKTKILYRDRDYH 155

Query: 135 GRTFGALTATGQEKYHKGFGPLLAGFKYVP------------------------LNDIEA 170
           G T  A++A GQE+ +  +GP    F  VP                         N IE 
Sbjct: 156 GSTLAAMSAGGQEERNMQYGPFAPDFVKVPHCMEYRKHELGLEHLSGKEFGIAAANQIEE 215

Query: 171 LY-EAVDDEVCAIMLEVIQGEGGIHEATPEYVKAVRKICDENDLLFILDEVQTGIGRTGK 229
           +      D V A+ LE +   GG+ EA   Y   V++IC + D+L  +DEV  G+GRTG 
Sbjct: 216 IILREGPDTVGALCLEPVTAGGGVIEAPEGYWPRVQEICKQYDILLHIDEVVCGVGRTGT 275

Query: 230 LFGYEHYGVVPDIMTLAKGLGGGF-PIGAIVAKEDKAVF--------KPGDH---ASTFG 277
            FGY+HYG+ PD +T+AKG+  G+  I  +V  E  AVF         P ++    STFG
Sbjct: 276 WFGYQHYGIQPDFVTMAKGVASGYAAIACLVTTE--AVFDMFKDDASDPMNYFRDISTFG 333

Query: 278 GNPLACAAGIAVLNEVTKDGFLEGVDKKGKYFREGLETLQKKHKVVKEIRGKGLMVGCE- 336
           G     AA +  +  +  +  L+     G   +  LE L +KH+V+ ++RGKGL +G E 
Sbjct: 334 GCTAGPAAALVNMQIIEDENLLDNCTAMGARMKSNLEALMEKHQVIGDVRGKGLFIGAEL 393

Query: 337 ---------VDLEDASEIVLKALEKGLLINSVS------HNVLRFVPPLIVTEEEIDEAL 381
                    VD + A  +V +   + ++I   +      +N L F P LIVT E++D+  
Sbjct: 394 VADRDTKEPVDEKLAQAVVAECGNQNVIIGVTNRSIPGKNNTLCFSPALIVTPEDVDKIT 453

Query: 382 QILDDVLSEI 391
             +D  L+++
Sbjct: 454 DAVDVALTKV 463


Lambda     K      H
   0.319    0.139    0.405 

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: 455
Number of extensions: 32
Number of successful extensions: 6
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: 393
Length of database: 465
Length adjustment: 32
Effective length of query: 361
Effective length of database: 433
Effective search space:   156313
Effective search space used:   156313
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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