GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:351200
          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:

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