GapMind for Amino acid biosynthesis

 

Alignments 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)



>MicrobesOnline__882:207019
          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.

Links

Downloads

Related tools

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