GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Galbibacter marinus ck-I2-15

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_008990092.1 I215_RS01065 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000300875.1:WP_008990092.1
          Length = 396

 Score =  380 bits (975), Expect = e-110
 Identities = 193/395 (48%), Positives = 273/395 (69%), Gaps = 4/395 (1%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVK-DGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63
           TI D +   K+ ++RVDFNVP+  D  V D TRI AA PTI   LE+G   IL+SHLGRP
Sbjct: 3   TIEDFNFNNKKALIRVDFNVPLDGDFNVTDTTRIEAAKPTIVKVLEEGGSAILMSHLGRP 62

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           KG+ S E SL  +  ++SE++G +VKFV   +G + ++A ++L+ GEVLLLEN RFH  E
Sbjct: 63  KGKKSDELSLKHIVAKVSEIIGVQVKFVDQSIGKDAEQAAKDLQPGEVLLLENLRFHSEE 122

Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS--VAGFLMEKEIKFLSKV 181
              +   A+  + L D++VNDAFGTAHRAHAS   +A++       G+L+ KEI+ ++KV
Sbjct: 123 EAGEESFAEALSKLGDVYVNDAFGTAHRAHASTTIVAKYFGQNKCFGYLLAKEIEAIAKV 182

Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241
             + EKP   +LGG+KVS KI +I N+++K D ++IGG M +TF+KA G ++G S  E+D
Sbjct: 183 MESGEKPVTAILGGSKVSSKITIIENILDKVDHLIIGGGMTYTFIKAQGGKIGDSICEDD 242

Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETI 301
           K +LA  +L+ A+ KGV++ LPVD + A       + ++V + + IP+GW GLD GP+T+
Sbjct: 243 KQELALRILKDAQAKGVKVHLPVDVLAANDFNNDADTQIVDVKE-IPDGWQGLDAGPKTL 301

Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361
           E FK+ + ++KT++WNGP+GVFE+  FA+GT  +   I   T+ GA ++VGGGDS AAV 
Sbjct: 302 ENFKEVILESKTILWNGPIGVFEMPSFAKGTIAIGNYIDQATKDGAFSLVGGGDSVAAVK 361

Query: 362 KFGLEDKFSHVSTGGGASLEFLEGKELPGIASIAD 396
           +FG EDK S+VSTGGGA LE LEGK LPGIA+I +
Sbjct: 362 QFGFEDKVSYVSTGGGAMLESLEGKTLPGIAAILE 396


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: 652
Number of extensions: 37
Number of successful extensions: 4
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 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