GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Pseudomonas fluorescens GW456-L13

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate PfGW456L13_927 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_927 Omega-amino
           acid--pyruvate aminotransferase (EC 2.6.1.18)
          Length = 454

 Score =  756 bits (1953), Expect = 0.0
 Identities = 351/448 (78%), Positives = 404/448 (90%)

Query: 7   NAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVN 66
           N +TREWQ LS DHHL PF+D+KQL EKG RIIT A+GVY+WDSEGNKILD MAGLWCV 
Sbjct: 5   NPQTREWQTLSNDHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVA 64

Query: 67  VGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEA 126
           +GYGR+EL  AA++QMRELP+YNLFFQTAHPPV+ELAKAIAD+APEGMNHVFFTGSGSE 
Sbjct: 65  IGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAIADIAPEGMNHVFFTGSGSEG 124

Query: 127 NDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHI 186
           NDT+LRMVRHYWA KGQP KKV+I R NGYHGSTVAG SLGGM  +HEQGD PIPGIVHI
Sbjct: 125 NDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHI 184

Query: 187 AQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWP 246
           AQPYW+ EGG+M+P+EFGVWAA QLE+KILEVG +NV AFIAEPIQGAGGVI+PP+TYWP
Sbjct: 185 AQPYWFAEGGEMTPEEFGVWAANQLEEKILEVGVDNVGAFIAEPIQGAGGVIIPPETYWP 244

Query: 247 KIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVR 306
           +I+EILAKYDILF+ADEVICGFGRTGEWFGS +Y   PD+M IAKGLTSGYIPMGG++VR
Sbjct: 245 RIKEILAKYDILFVADEVICGFGRTGEWFGSDFYDLKPDMMTIAKGLTSGYIPMGGLIVR 304

Query: 307 DEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQEL 366
           DE+V+VLN+GG+F HGFTYSGHPVAAAV LENIRILR+EKI+E+VK+ETAPYLQKR +EL
Sbjct: 305 DEVVDVLNEGGDFNHGFTYSGHPVAAAVGLENIRILRDEKIVERVKSETAPYLQKRLREL 364

Query: 367 ADHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIIS 426
            DHPLVGE RGVG++ A+ELV++K TR+RF  KGVGM+CR+ CF NGLIMRAVGDTMII+
Sbjct: 365 NDHPLVGEVRGVGLLGAIELVQDKATRKRFEGKGVGMICRQFCFDNGLIMRAVGDTMIIA 424

Query: 427 PPLVIDPSQIDELITLARKCLDQTAAAV 454
           PPLVI P++IDEL+T ARKCLD T +A+
Sbjct: 425 PPLVITPAEIDELVTKARKCLDLTLSAL 452


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: 823
Number of extensions: 36
Number of successful extensions: 1
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: 454
Length adjustment: 33
Effective length of query: 423
Effective length of database: 421
Effective search space:   178083
Effective search space used:   178083
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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