Alignments for a candidate for iorAB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Acidovorax sp. GW101-3H11

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate Ac3H11_1196 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits

Query= reanno::Marino:GFF880
         (1172 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1196
          Length = 1191

 Score = 1027 bits (2656), Expect = 0.0
 Identities = 541/1190 (45%), Positives = 760/1190 (63%), Gaps = 42/1190 (3%)

Query: 1    MSADTPQ-----LDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVS 55
            M+A  P+     L+   L+D+Y  + GR F++G QALVR+P++Q   D   GLNTAG +S
Sbjct: 1    MNAPLPESVRKALETVTLDDKYSLDHGRAFMSGVQALVRLPMLQRQRDAVAGLNTAGFIS 60

Query: 56   GYRGSPLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVET-DEDRQVEGVF 114
            GYRGSPLG  DQALW AK  L  N I F P +NE+L AT + GTQQ++   + ++ +GVF
Sbjct: 61   GYRGSPLGTYDQALWAAKKHLAANNIVFQPGVNEELGATAVWGTQQLDLYPQSKKFDGVF 120

Query: 115  GLWYGKGPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMP 174
            G+WYGKGPGVDR  D  KH    G++ HGGV+ +AGDDH   SS+  HQSD  F +   P
Sbjct: 121  GIWYGKGPGVDRCSDVFKHANMAGTAKHGGVIAIAGDDHISKSSTAAHQSDHIFKACGTP 180

Query: 175  TINPANIAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTA 233
               P+++ E L+ GL  +A+SR+SG W G K I E VES++S+ I P     V P+DF  
Sbjct: 181  VFFPSSVQEILDMGLHAFAMSRFSGVWSGMKTIQEVVESSSSINIDPDRVKIVMPEDFVM 240

Query: 234  PESGLHYRWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLD 293
            P  GLH RWPD P  Q    +++K  A  A+ RAN+++  + + K  RFGI+ +GK + D
Sbjct: 241  PPGGLHIRWPDAPLEQEARLMDYKWYAALAYIRANKLNYNVIEGKNDRFGIIASGKAYND 300

Query: 294  LLEALDLLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQI 353
              +AL  LG+D+D  R +G+ ++KV +VWPLE     DF  G +E+LV+EEKR +IE Q+
Sbjct: 301  TRQALVDLGLDDDTCRQLGIRVHKVNVVWPLEATITRDFAQGLQEILVVEEKRQVIEYQL 360

Query: 354  KEYMSEPDRPGEVLITGKQDE-----------LGRP----LIPYVGELSPKLVAGFLAAR 398
            KE +          + GK DE           +  P    L+    +L+P ++A  +A R
Sbjct: 361  KEELYNWRADVRPNVLGKFDEPEGDATGGEWSMPNPSQNWLLRAKADLTPAIIAKAIAKR 420

Query: 399  LGRF-FEVDFSERMAEISAMTTAQDPGGVK-------RMPYFCSGCPHNTSTKVPEGSKA 450
            L +     D   RM    A+  A + G  +       R P+FCSGCPHNTST+VPEGS+A
Sbjct: 421  LKKLGVSSDIIARMDSRIAVIEASERGMAELKVDTGERAPWFCSGCPHNTSTRVPEGSRA 480

Query: 451  LAGIGCHFMASWM-GRNTESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAI 509
            +AGIGCH+MA+WM  R T +  QMGGEGV W+G++ +T + HVF NLG+GTYFHSG +AI
Sbjct: 481  VAGIGCHYMANWMPDRKTSTFTQMGGEGVTWVGQAPFTTDAHVFANLGDGTYFHSGLLAI 540

Query: 510  RQAVAAGINITYKILFNDAVAMTGGQPVDGQI---TVDRIAQQMAAEGVNRVVVLSDEPE 566
            RQ++AAG +ITYK+L+NDAVAMTGGQ V  +    +V +I   + +EGV ++++++DEP+
Sbjct: 541  RQSIAAGTSITYKVLYNDAVAMTGGQTVGERPEGHSVLQIMNSLKSEGVVKLIIVTDEPQ 600

Query: 567  KYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPA 626
            KYDG        VT H R ELD +QR+ R+I GCTV+IYDQTCA EKRRRRKR     P 
Sbjct: 601  KYDGV--ALAAGVTVHHRDELDTLQRQFREIKGCTVIIYDQTCATEKRRRRKRGTLATPD 658

Query: 627  KRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTI 686
            K   IN  VCEGCGDCS +SNCLSV P +TE GRKR+I+QS+CNKD+SCVNGFCPSFVT+
Sbjct: 659  KTVVINDLVCEGCGDCSTKSNCLSVEPVETEFGRKRRINQSTCNKDYSCVNGFCPSFVTV 718

Query: 687  EGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAH 746
            EGG+L+K +    G +    L  IP P LP    ++ ++VGGVGGTGV+T+G L+ MAAH
Sbjct: 719  EGGKLKKPKKEKKGDLSA--LPSIPEPVLPVAEAAWGIVVGGVGGTGVITIGSLLGMAAH 776

Query: 747  LESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKA 806
            L+ +G    D  G AQKGG   S++++A  P+ ++  ++   +AD VI CD +VA+ +  
Sbjct: 777  LDGKGVITQDAGGLAQKGGATWSHIQIANRPEAIYTTKVDTAKADLVIGCDSIVAAHKYT 836

Query: 807  LSVLRPNHTRIVANEAELPTADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEK 866
            L+V++P  T +  N    PTA +V   D           +  AVG       DA  +A +
Sbjct: 837  LTVMQPGRTFVALNTHSTPTAAFVTNPDWQFPGANCDSAIAAAVGAGGVGSFDAEQVATQ 896

Query: 867  LMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAV 926
            L+GD++++N +MLG+AWQKG +PL+ A+LM+A+ELNGV +D NK AF WGR  A D ++V
Sbjct: 897  LLGDSIYTNPLMLGYAWQKGRVPLTLASLMRAMELNGVQVDNNKAAFEWGRRCAHDLASV 956

Query: 927  TDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGET 986
              L     AQV++   +P+L E+I  R + L  YQN  +A +Y   V  V KA ES  + 
Sbjct: 957  QALF--QAAQVIQFVKKPSLTEMIAKRVEFLTGYQNAAYAAEYHAFVEKV-KATESRLDV 1013

Query: 987  NLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGET 1046
               L+ AVA+ L++ MAYKDEYEVARL  +  F  ++   FEGD+K+  HLAPP+ + + 
Sbjct: 1014 GTRLSEAVARYLFKLMAYKDEYEVARLHTDKAFTDKIVNMFEGDYKLVHHLAPPMTAKKN 1073

Query: 1047 DAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIG 1106
            D +G   K+ FGPWM  AF LLAK++GLRGTA+D F  + +R+++RA++ +Y++ +D + 
Sbjct: 1074 D-KGELVKQPFGPWMRSAFGLLAKMKGLRGTALDVFGKTEERRMERALIVEYRACIDELL 1132

Query: 1107 RELNASNYETFLQLAELPADVRGYGPVREQAAESIREKQTQLIKALDTGR 1156
              LNA N    +++A +P ++RGYG V+E+  ++ R K   L+    +G+
Sbjct: 1133 ATLNADNLALAVEIARIPEEIRGYGHVKERHLKAARPKWDGLMAQWRSGK 1182


Lambda     K      H
   0.319    0.136    0.405 

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: 2984
Number of extensions: 116
Number of successful extensions: 11
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: 1172
Length of database: 1191
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1144
Effective search space:  1287000
Effective search space used:  1287000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources