GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Bacteroides thetaiotaomicron VPI-5482

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 351200 BT1672 phosphoglycerate kinase (NCBI ptt file)

Query= BRENDA::P36204
         (654 letters)



>lcl|FitnessBrowser__Btheta:351200 BT1672 phosphoglycerate kinase
           (NCBI ptt file)
          Length = 419

 Score =  366 bits (939), Expect = e-105
 Identities = 199/417 (47%), Positives = 269/417 (64%), Gaps = 29/417 (6%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKDGV-VQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63
           TI   +  GK+  +RVDFNVP+ +   + DDTR+RAALPT+K  L  G  +I+ SHLGRP
Sbjct: 3   TIDKFNFAGKKAFVRVDFNVPLDENFNITDDTRMRAALPTLKKILADGGSIIIGSHLGRP 62

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           KG  + +FSL  + K LSELLG EV+F    +G+E       L+ GEVLLLEN RF+  E
Sbjct: 63  KGV-ADKFSLKHIIKHLSELLGVEVQFANDCMGEEAAVKAAALQPGEVLLLENLRFYAEE 121

Query: 124 T-----------------------KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIA 160
                                   ++  E  K  AS AD +VNDAFGTAHRAHAS   IA
Sbjct: 122 EGKPRGLAEDATDEEKAAAKKAVKESQKEFTKKLASYADCYVNDAFGTAHRAHASTALIA 181

Query: 161 QFIPS---VAGFLMEKEIKFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILI 217
           ++  +   + G+LMEKE+K + KV  + ++P+  ++GG+KVS KI +I NL+ K D ++I
Sbjct: 182 KYFDTDNKMFGYLMEKEVKAVDKVLNDIQRPFTAIMGGSKVSSKIEIIENLLNKVDNLII 241

Query: 218 GGAMMFTFLKALGKEVGSSRVEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVE 277
            G M +TF KA+G ++G S  E+DK+DLA +L++KAKEKGV +VL VDA IA        
Sbjct: 242 AGGMTYTFTKAMGGKIGISICEDDKLDLALDLIKKAKEKGVNLVLAVDAKIADAFSNDAN 301

Query: 278 KKVVRIDDGIPEGWMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVAL 337
            +   +D+ IP+GW GLDIGP+T E+F   + ++KT++WNGP GVFE ++F  G++ V  
Sbjct: 302 TQFCAVDE-IPDGWEGLDIGPKTEEIFANVIKESKTILWNGPTGVFEFENFTHGSRTVGE 360

Query: 338 AIAALTEKGAITVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           AI   T+ GA ++VGGGDS A VNKFGL    S+VSTGGGA LE +EGK LPGIA+I
Sbjct: 361 AIVEATKNGAFSLVGGGDSVACVNKFGLASGVSYVSTGGGALLEAIEGKVLPGIAAI 417


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: 688
Number of extensions: 45
Number of successful extensions: 6
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: 419
Length adjustment: 35
Effective length of query: 619
Effective length of database: 384
Effective search space:   237696
Effective search space used:   237696
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 preprint 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