Alignments for a candidate for patA in Halomonas xinjiangensis TRM 0175

GapMind for catabolism of small carbon sources

Alignments for a candidate for patA in Halomonas xinjiangensis TRM 0175

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_043526888.1 JH15_RS03040 aspartate aminotransferase family protein

Query= BRENDA::Q9I6J2
         (456 letters)



>NCBI__GCF_000759345.1:WP_043526888.1
          Length = 459

 Score =  597 bits (1539), Expect = e-175
 Identities = 285/445 (64%), Positives = 349/445 (78%), Gaps = 2/445 (0%)

Query: 10  TREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGY 69
           T + +AL   HHL PFTDYK L E+G+RI+T A+G+YI DSEGN+ILD MAGLWCVN+GY
Sbjct: 3   TADLKALDSAHHLHPFTDYKALGEEGSRIVTHAQGIYIHDSEGNRILDGMAGLWCVNLGY 62

Query: 70  GREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDT 129
           GR ELV+AA+ QM +LP+YN FF++ HPP V+LAK +  +AP  MN VFFTGSGSEANDT
Sbjct: 63  GRAELVEAASAQMSQLPYYNNFFKSTHPPAVKLAKMLCGLAPGHMNRVFFTGSGSEANDT 122

Query: 130 VLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQP 189
           VLRMVR YW  KGQP K+ VI R N YHGSTVAGVSLGGM  +  QG   +P I HI QP
Sbjct: 123 VLRMVRRYWELKGQPDKRWVIARDNAYHGSTVAGVSLGGMSPMRNQGGPLVPDIAHIRQP 182

Query: 190 YWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIR 249
           YW+GEG DM+P+ FG   A  LE+KILE+G ENVAAFIAEP+QGAGG I+PP++YWP I+
Sbjct: 183 YWFGEGRDMTPEAFGRVCAADLERKILELGVENVAAFIAEPVQGAGGAIIPPESYWPAIK 242

Query: 250 EILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEI 309
            IL KYDIL + DEVICGFGR GEWFGSQ+Y   PDLMP+AKGL+SGY+P+GGV+V D +
Sbjct: 243 AILDKYDILLVIDEVICGFGRLGEWFGSQHYSLEPDLMPVAKGLSSGYLPIGGVLVGDRV 302

Query: 310 VEVL-NQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELAD 368
            + L  +GGEF+HGFTYSGHPV A VAL N++ILR+E +I++V+ +  PYL KRW EL +
Sbjct: 303 ADTLIEEGGEFFHGFTYSGHPVCATVALRNLQILRDEAVIDRVRDDIGPYLAKRWAELGE 362

Query: 369 HPLVGEARGVGMVAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIMRAVGDTMIISP 427
           HPLVGEAR +G++ ALELV +K++ +RF     VG LCR+  F  GL+MR+VGDTMIISP
Sbjct: 363 HPLVGEARSLGLIGALELVADKQSGQRFPQAFAVGNLCRDISFDKGLVMRSVGDTMIISP 422

Query: 428 PLVIDPSQIDELITLARKCLDQTAA 452
           PLVI   Q+DEL+ LA + LD TAA
Sbjct: 423 PLVIRHDQVDELVALAWQALDATAA 447


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: 732
Number of extensions: 34
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: 459
Length adjustment: 33
Effective length of query: 423
Effective length of database: 426
Effective search space:   180198
Effective search space used:   180198
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources