GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Phaeobacter inhibens BS107

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF3387 PGA1_c34400 aminotransferase class-III

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__Phaeo:GFF3387 PGA1_c34400 aminotransferase
           class-III
          Length = 464

 Score =  594 bits (1531), Expect = e-174
 Identities = 294/453 (64%), Positives = 348/453 (76%), Gaps = 4/453 (0%)

Query: 5   ITN-AKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLW 63
           ITN   T E QAL   HH+ PFT   +L EKGARIIT+A GV + DSEGN+ILDAMAGLW
Sbjct: 4   ITNHLPTAELQALDAAHHMHPFTANGELAEKGARIITRARGVTLTDSEGNEILDAMAGLW 63

Query: 64  CVNVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSG 123
           CVN+GYGR+EL   A RQMRELP+YN FFQT H P + LA  IA++AP+G+NHVFF GSG
Sbjct: 64  CVNIGYGRDELADVAARQMRELPYYNTFFQTTHAPAIALAAKIAELAPDGLNHVFFAGSG 123

Query: 124 SEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGI 183
           SEANDT +RMVRHYWA K +P K V+I R NGYHGS+V   SLGGM A+HEQG  PIP I
Sbjct: 124 SEANDTNIRMVRHYWAMKAKPTKSVIISRKNGYHGSSVGSGSLGGMTAMHEQGGLPIPDI 183

Query: 184 VHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDT 243
            HI QP W+ EGGDMS ++FG+  A++LE+ ILE+GE+ VAAFIAEP+QGAGGVIVPP T
Sbjct: 184 HHINQPNWWAEGGDMSAEDFGLARAQELEQAILELGEDRVAAFIAEPVQGAGGVIVPPAT 243

Query: 244 YWPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGV 303
           YWP+I+ I  KY+IL IADEVICGFGRTG WFGSQ  G  PD+M IAKGL+SGY P+GG 
Sbjct: 244 YWPEIQRICDKYEILLIADEVICGFGRTGNWFGSQSVGIRPDIMTIAKGLSSGYAPIGGS 303

Query: 304 VVRDEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRW 363
           +V DEI  V+   GEF HG+TYSGHPVAAAVALEN+RIL EE II  V+   APYL+++W
Sbjct: 304 IVSDEIASVIG-SGEFNHGYTYSGHPVAAAVALENLRILEEENIIGHVRDVAAPYLKEKW 362

Query: 364 QELADHPLVGEARGVGMVAALELVKNKKTRERFTDKG--VGMLCREHCFRNGLIMRAVGD 421
           + LADHPLVGEA+ VGM+ ++ L  NK TR  F  +G  VG +CRE CF N L+MR VGD
Sbjct: 363 EALADHPLVGEAKIVGMMGSIALTPNKATRAGFAAEGGTVGYICRERCFANNLVMRHVGD 422

Query: 422 TMIISPPLVIDPSQIDELITLARKCLDQTAAAV 454
            MIISPPLVI P +ID LI  AR+ LD+  AA+
Sbjct: 423 RMIISPPLVITPEEIDTLIARARQSLDECYAAL 455


Lambda     K      H
   0.320    0.138    0.425 

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: 712
Number of extensions: 26
Number of successful extensions: 3
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: 456
Length of database: 464
Length adjustment: 33
Effective length of query: 423
Effective length of database: 431
Effective search space:   182313
Effective search space used:   182313
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 (21.8 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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