GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Paraburkholderia bryophila 376MFSha3.1

Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate H281DRAFT_01831 H281DRAFT_01831 DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain

Query= reanno::acidovorax_3H11:Ac3H11_1015
         (396 letters)



>FitnessBrowser__Burk376:H281DRAFT_01831
          Length = 414

 Score =  342 bits (877), Expect = 1e-98
 Identities = 178/397 (44%), Positives = 257/397 (64%), Gaps = 10/397 (2%)

Query: 2   QFADRLNNVETSAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIRAASNAALAEEPGAAL 61
           +F     N   S IRELFK LG+PG+ISFAGG+P S +FDV+G++ A   A  ++P + L
Sbjct: 14  EFTAPFQNPSGSPIRELFKYLGEPGMISFAGGYPASDLFDVDGLQQAEARAY-QDPNSCL 72

Query: 62  QYGATEGYNPLREQLAAFMTSKGAKDVAADNLIVTTGSQQALDLLGKTLISPGDKVIVEG 121
           QYG T+G   L+ +L + M  +G    A + ++VTTGSQQ LDLL + L+SPGD V  E 
Sbjct: 73  QYGPTDGLPRLKHELISLMARRGVP-CALNEMLVTTGSQQGLDLLLRVLVSPGDVVFTEQ 131

Query: 122 PTFLATIQCFRLYGAELISAPIDGNGVKTDELEKLIAEHK---PKFVYLIPTFGNPSGAM 178
           P + AT+Q  +L  A++++ P+D +G+  D L +L+A  +   PK +Y +PTF NP+GA 
Sbjct: 132 PAYPATLQALKLQQAKIVTVPVDAHGLDVDHLAELLASGRVARPKLLYTVPTFANPTGAT 191

Query: 179 LSLERRKAVLEMAVKHNTLIVEDDPYGDLYFGDAPPPSLLNLSATVPGSRELLVHCGSLS 238
           ++ ERR A+L++AV++  LIVEDDPYGDL F     PS+++L+A V GSR+ +VH  SLS
Sbjct: 192 ITRERRIALLKLAVQYKFLIVEDDPYGDLRFSGVAVPSIISLAAEVEGSRDWVVHFASLS 251

Query: 239 KVLSPGLRVGWMIAPAELLGKATMCKQFSDAHTSTFAQATAAQYLKAGRMPGTLANVRKV 298
           K+++PGLRVGW IAPAE+  +  + KQ  D  ++ + QA AA+YL  G +   L  + ++
Sbjct: 252 KIVAPGLRVGWTIAPAEITRRCVIAKQTVDLCSAPWTQAIAAEYLADGALERHLPRITEM 311

Query: 299 YAERAQAMGDALRKELGDAIEFVQPQGGLFVWARLTGAGGKVADGNVLAKRAIEKGVAFV 358
           Y  + +A+ +ALR + GD ++F +P GG+FVWAR+ G      D + L + AIE  V FV
Sbjct: 312 YGRKCEALCEALRSQFGDTLQFHRPDGGMFVWARIEG-----IDASALLQHAIENKVMFV 366

Query: 359 PGTPFFCANPDHATFRLSFATADVDKIREGVARLGQA 395
           PG  FF    D A+ RLSFA   +  I EG  RL +A
Sbjct: 367 PGKAFFADRIDPASLRLSFAAPGIADIEEGAKRLRRA 403


Lambda     K      H
   0.319    0.136    0.394 

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: 504
Number of extensions: 30
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: 396
Length of database: 414
Length adjustment: 31
Effective length of query: 365
Effective length of database: 383
Effective search space:   139795
Effective search space used:   139795
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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