GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Halomonas xinjiangensis TRM 0175

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_043532756.1 JH15_RS17385 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000759345.1:WP_043532756.1
          Length = 387

 Score =  347 bits (890), Expect = e-100
 Identities = 190/396 (47%), Positives = 267/396 (67%), Gaps = 18/396 (4%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60
           + KMT  D+DL G+RV++R D NVP+K+G V  D R+RA LPTIK A E GAKV+L+SHL
Sbjct: 3   VRKMT--DLDLAGQRVLIREDLNVPIKNGRVTSDARLRACLPTIKAAAEAGAKVMLMSHL 60

Query: 61  GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           GRP +GEP+ EFSLAPVA+ L  LL + V+ V      +      EL +GEV LLEN RF
Sbjct: 61  GRPTEGEPADEFSLAPVAEHLGTLLDRPVRLV-----KDYLDYSPELADGEVALLENVRF 115

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSV-AGFLMEKEIKFL 178
           + GE K+D  LAK +A+L D++V DAFGTAHRA AS  G+A+F P+  AG L+ +E++ L
Sbjct: 116 NSGEKKDDEALAKRYAALCDVYVMDAFGTAHRAQASTHGVARFAPTACAGPLLAQELEAL 175

Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238
            K   NP++P V ++GG+KVS K+ V+  L EK D++++GG +  TF+ A G  VG S  
Sbjct: 176 EKALANPKRPMVAIVGGSKVSTKLDVLNALAEKCDQLIVGGGIANTFIAAAGYNVGKSLY 235

Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298
           E+D +D A   +EK     V+I LP D V+A +     +  VV+  D + +  M LD+GP
Sbjct: 236 EKDLVDKASAFMEK-----VDIPLPTDVVVATEFSESAD-AVVKGVDHVNDEEMILDVGP 289

Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358
            + E     L +A T++WNGP+GVFEID F +GT+ +A AIAA     A ++ GGGD+ A
Sbjct: 290 MSAEKLGDLLKEAGTILWNGPVGVFEIDQFGQGTQSLAQAIAA---SSAFSIAGGGDTLA 346

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           A++K+G+ D+ S++STGGGA LE++EGK LP +A++
Sbjct: 347 AIDKYGIADQVSYISTGGGAFLEYVEGKTLPAVAAL 382


Lambda     K      H
   0.317    0.137    0.386 

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: 570
Number of extensions: 28
Number of successful extensions: 7
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: 654
Length of database: 387
Length adjustment: 34
Effective length of query: 620
Effective length of database: 353
Effective search space:   218860
Effective search space used:   218860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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