GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Caulobacter crescentus NA1000

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate CCNA_03359 CCNA_03359 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03359 CCNA_03359 phosphoglycerate
           kinase
          Length = 396

 Score =  364 bits (935), Expect = e-105
 Identities = 194/396 (48%), Positives = 261/396 (65%), Gaps = 12/396 (3%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64
           T+   DL GKR ++RVDFNVPV  G V DDTR++AALPTI++  ++GAKV+LL+H  RPK
Sbjct: 5   TLDTADLAGKRALVRVDFNVPVDGGKVADDTRLKAALPTIRFLADKGAKVVLLAHFDRPK 64

Query: 65  GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124
           G+  PE SLA VA+ L+ LLG  V FV   VG    + V  L +G V LLEN RFH GE 
Sbjct: 65  GKVVPEMSLAFVAEPLAALLGAPVAFVGDCVGPAAAEVVNGLADGGVALLENVRFHAGEE 124

Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184
           KND E AK  A+  D++VNDAF  AHRAHAS  G+A+ +P+  G  M++E++ L     N
Sbjct: 125 KNDAEFAKALAANGDVYVNDAFSAAHRAHASTEGLAKLLPAYPGVSMQRELEALDAALGN 184

Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244
           P+KP + ++GG+KVS K+ ++ NL+ K DR+ IGG M  TFL A G +VG S  E+D  D
Sbjct: 185 PKKPVIGIVGGSKVSTKLDLLNNLVAKLDRLAIGGGMANTFLFAQGHDVGGSLCEKDLAD 244

Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKV-----VRIDDGIPEGWMGLDIGPE 299
            A+E++EKAK  G E++LPVD V+A+K+ PGVE  V     V+ DD I      LD GPE
Sbjct: 245 TAREIMEKAKAAGCELLLPVDVVVAKKVAPGVETAVRSLSEVQADDLI------LDAGPE 298

Query: 300 TIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAI-TVVGGGDSAA 358
           + +     +  + T++WNGP+GVFE+  F E T   A   A+L + G I  V GGGD+ A
Sbjct: 299 SAKRLLAAMDQSLTLIWNGPLGVFEVPPFDEATVSAAKHAASLAKSGKIVAVAGGGDTVA 358

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           A+N  G+   F+ VST GGA LE++EGK LPG+A++
Sbjct: 359 ALNHAGVSADFTFVSTAGGAFLEWMEGKTLPGVAAL 394


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: 627
Number of extensions: 35
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: 654
Length of database: 396
Length adjustment: 34
Effective length of query: 620
Effective length of database: 362
Effective search space:   224440
Effective search space used:   224440
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 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 paper from 2022 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