GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ofoa in Desulfovibrio vulgaris Hildenborough

Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha; Short=OFOR2; EC 1.2.7.11 (characterized, see rationale)
to candidate 207019 DVU1569 pyruvate ferredoxin oxidoreductase, alpha subunit

Query= uniprot:OFOA2_AERPE
         (642 letters)



>lcl|MicrobesOnline__882:207019 DVU1569 pyruvate ferredoxin
           oxidoreductase, alpha subunit
          Length = 578

 Score =  229 bits (584), Expect = 3e-64
 Identities = 189/621 (30%), Positives = 294/621 (47%), Gaps = 87/621 (14%)

Query: 5   SLIIGGPQGGGIESAGQIAIKSMVLLGYEVLGSREYHSNIMGAHSYYHLRVQQHRPRSLK 64
           S++IGG  G G+ + G + +++++  GY VL ++ Y S + G H+ Y++RV      +  
Sbjct: 7   SIVIGGEAGQGLVTIGDMLVRTLIRSGYGVLVAQHYMSRVRGGHNTYNIRVGAGDVLAPT 66

Query: 65  LPVDGVLALDAESVFTHFRDVRPGGILVYDPGTKSTRVDAIQ-PMAGPLKKRLKSLFDSR 123
             V  ++ALD  +V T        G+L+ D       ++A++ P A              
Sbjct: 67  DDVHVLVALDQRTV-TEQGPRLGDGLLILDERLDPGSLNALRVPFAA------------- 112

Query: 124 GMQPVVESAVKLAEEAGARIVGLPLKEMLKTLSERTGAPVARVSRALNTLGLASMLYMLG 183
                              + G PL E                    N   L  +  +LG
Sbjct: 113 -------------------LAGRPLYE--------------------NIAALGVLAALLG 133

Query: 184 VPVEYIEKAISLQFAGK-EKVINMNVEAVRIAVDYVRE--AFGEPESRLPPGPRRGQTMM 240
           +    +++ +   F  K + VI  N+E +  A  +  +  A  EP S  P GP      M
Sbjct: 134 LERAPVDRLVGEAFHKKGDDVITRNLEVLEAAWRWASDHRAASEPLSA-PEGPTG---RM 189

Query: 241 VATGNDLVAMGKIVGGLGVITYYPITPSSDEALYVEKHSYISIDGPLAEKLGYDKIAVAI 300
           +  GN+ +A+G +  G+    +YP+TP++  A  +  H         AE++G     V +
Sbjct: 190 MLQGNEAIALGALAAGVKFCAFYPMTPATSVAQNLILH---------AERMG-----VVV 235

Query: 301 VQMEDELASINAVLGAAAAGARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTLWMRAGPS 360
            Q EDE+A++N VLGA+ AGARA   TSG GF+LM E VSLA   E PVV+ L  R GP+
Sbjct: 236 EQAEDEIAAMNMVLGASYAGARALVPTSGGGFALMTEGVSLAGVMEQPVVIVLAQRPGPA 295

Query: 361 TGMPTRTGQQDLLHSIFSGHGDAPKIVLASGDHVEAFYDAIKAFNWAEEFQTPVIHLLDK 420
           TG+PTRT Q DL  ++++GHG+ P+++ A     + F+    AF+ AE FQ P   L D+
Sbjct: 296 TGLPTRTEQADLDLALYAGHGEFPRVIFAPATPEDCFHLTYAAFDLAERFQIPAFVLTDQ 355

Query: 421 YLASSMVSLAREDLDPSKVPITRGKLLDNPPAD--YRRYEVVEDGISPRARLG-SATMVI 477
           YLA S   +A  DLD            D  P    Y+RYE+ + GISPR   G S ++V+
Sbjct: 356 YLADSYRPVAPFDLDALPPLAEPDFSTDKGPEGDRYKRYELTKSGISPRRIPGFSKSLVL 415

Query: 478 TGL-EHDEYGYATEDPVMREIMMFKRERKFKVIEE-RIPDEEKAVLHGDSEASVALVSFG 535
               EH E GY TED  +R  M  KR RK   +    +P        GD    + L  +G
Sbjct: 416 ADCHEHTEQGYITEDAGLRIAMSDKRLRKGDGLRSMALPPR----CFGDEAPDLLLACWG 471

Query: 536 STKQPILEALEMLRDEGVRARFAQVRLLYPF-PGRLVEEMLEGVEKVIMVEQNLLGQLAM 594
           S++  ++EA + LR  G +        ++P  P + +    E  E V+ +E N +GQ + 
Sbjct: 472 SSEGAVVEAAQRLRARGRKVGVLSFTQVWPLEPSQFLSRCGEASE-VVCIEGNAIGQFSR 530

Query: 595 LLRAHTSIKPDSSIVKINGRP 615
           LLR    +    ++++ +GRP
Sbjct: 531 LLRL-GGVTVGRTLLRYDGRP 550


Lambda     K      H
   0.318    0.135    0.380 

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: 841
Number of extensions: 43
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 642
Length of database: 578
Length adjustment: 37
Effective length of query: 605
Effective length of database: 541
Effective search space:   327305
Effective search space used:   327305
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or see changes to Amino acid biosynthesis since the publication.

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