GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Aquimarina longa SW024

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_062055072.1 N456_RS06325 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_001401755.1:WP_062055072.1
          Length = 395

 Score =  383 bits (984), Expect = e-111
 Identities = 202/395 (51%), Positives = 271/395 (68%), Gaps = 5/395 (1%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKDGV-VQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63
           TI D + + K+ ++RVDFNVP+ +   V DDTRI+AA PTI   LE G   +L+SHLGRP
Sbjct: 3   TINDFNFENKKALIRVDFNVPLNEKFEVTDDTRIQAAKPTIIKVLEDGGSAVLMSHLGRP 62

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           KG    EFSL  +  ++++ +G +VK+V   VG + + AV  L  GEVLLLEN RFH  E
Sbjct: 63  KGVQD-EFSLRHIVDKVADTVGVQVKYVDNCVGQKAEDAVAALNPGEVLLLENLRFHSNE 121

Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS--VAGFLMEKEIKFLSKV 181
           T  D   A+  + L DI+VNDAFGTAHRAHAS   +AQF P     G L+ KEI  + KV
Sbjct: 122 TDGDVAFAEQLSKLGDIYVNDAFGTAHRAHASTTIVAQFFPKHKCFGSLLAKEIDSIEKV 181

Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241
             + EKP   VLGG+KVS KI +I N+++K D ++IGG M +TF+KA G ++G S  E+D
Sbjct: 182 LKSGEKPITAVLGGSKVSSKITIIENILDKVDHLIIGGGMTYTFIKAKGGQIGGSICEDD 241

Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETI 301
           K +LA ++L+KA EKGV+I LPVD + A   +     KV+ +D  IP+ W GLD GPET+
Sbjct: 242 KQELALDILKKAAEKGVQIHLPVDVLGADAFDNNANTKVIDVDT-IPDNWQGLDAGPETM 300

Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361
           + F   +  +KT++WNGP+GVFE+++FA+GT  +  +IA  TEKGA ++VGGGDS AAV 
Sbjct: 301 KNFHDVILKSKTILWNGPLGVFEMENFAKGTIALGHSIAEATEKGAFSLVGGGDSVAAVK 360

Query: 362 KFGLEDKFSHVSTGGGASLEFLEGKELPGIASIAD 396
           +FG  +K S+VSTGGGA LE LEGK LPGIA+I +
Sbjct: 361 QFGFGNKVSYVSTGGGAMLESLEGKTLPGIAAIEE 395


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: 635
Number of extensions: 36
Number of successful extensions: 5
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: 395
Length adjustment: 34
Effective length of query: 620
Effective length of database: 361
Effective search space:   223820
Effective search space used:   223820
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