GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Pseudomonas fluorescens FW300-N2E3

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate AO353_08585 AO353_08585 aminotransferase

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08585
          Length = 454

 Score =  753 bits (1943), Expect = 0.0
 Identities = 350/448 (78%), Positives = 402/448 (89%)

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

Query: 67  VGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEA 126
           +GYGR+EL  AA++QMRELP+YNLFFQTAHPPV+ELAKAI+D+APEGMNHVFFTGSGSE 
Sbjct: 65  IGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEG 124

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

Query: 187 AQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWP 246
            QPYW+GEGGDM+P+EFG+WAA QLE+KILE+G + V AFIAEPIQGAGGVI+PPD+YWP
Sbjct: 185 PQPYWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWP 244

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

Query: 307 DEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQEL 366
           DE+VEVLN+GG+F HGFTYSGHPVAAAVALENIRILREEKIIE V+AETAPYLQKR +EL
Sbjct: 305 DEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLREL 364

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

Query: 427 PPLVIDPSQIDELITLARKCLDQTAAAV 454
           PPLVI  ++IDEL+T ARKCLD T +A+
Sbjct: 425 PPLVITKAEIDELVTKARKCLDLTLSAL 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: 838
Number of extensions: 42
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:

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