Alignments for a candidate for iorAB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Cupriavidus basilensis 4G11

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate RR42_RS34245 RR42_RS34245 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Cup4G11:RR42_RS34245
          Length = 1186

 Score = 1127 bits (2914), Expect = 0.0
 Identities = 602/1179 (51%), Positives = 787/1179 (66%), Gaps = 42/1179 (3%)

Query: 2    SADTPQLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSP 61
            SA    L    L+D+Y  E GRV+L+GTQALVR+P++Q A D   GLNTAG +SGYRGSP
Sbjct: 7    SAQQDALASVSLDDKYTLEKGRVYLSGTQALVRLPMLQKARDLAAGLNTAGFISGYRGSP 66

Query: 62   LGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKG 121
            LG VDQALW+AK  L  + + F P +NEDLAAT + GTQQV    D   +GVF +WYGKG
Sbjct: 67   LGGVDQALWKAKKHLAASDVVFQPGVNEDLAATAVWGTQQVNLFPDATRDGVFSMWYGKG 126

Query: 122  PGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANI 181
            PGVDR+ D LKH  + GS+ HGGVL++AGDDH   SSS+ HQS+   ++  +P + P+N+
Sbjct: 127  PGVDRSIDVLKHANSAGSAKHGGVLLLAGDDHAAKSSSVAHQSEHVLLASGIPVLYPSNV 186

Query: 182  AEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEI-PPAPDFVTPDDFTAPESGLHY 240
             EYL++GL G+A+SRYSG WV  K +++ VES ASVE+ P     V P+DF  PE GL+ 
Sbjct: 187  QEYLDYGLHGWAMSRYSGLWVSMKCVTDVVESTASVEVDPDRVRIVLPEDFAMPEGGLNI 246

Query: 241  RWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDL 300
            RWPD P  Q    ++HK  A  A+ RAN+++R + D+  ARFGI+T GK +LD+ +AL  
Sbjct: 247  RWPDPPLAQEARLLDHKWYAALAYIRANKLNRVVLDSPNARFGIMTAGKAYLDVRQALSD 306

Query: 301  LGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEP 360
            LG+D+D  R +G+ ++KVG VWPL+     +F  G EE+LV+EEKR I+E  +KE +   
Sbjct: 307  LGLDDDTCRRIGIRVFKVGCVWPLDAHDAREFATGLEEILVVEEKRQILEYALKEELYNW 366

Query: 361  DRPGEVLITGKQDELGRP-----------LIPYVGELSPKLVAGFLAARLGRF-FEVDFS 408
                   + GK DE G             L+P   ELSP L+A  +A RL +     D  
Sbjct: 367  RDDVRPKVYGKFDERGNHGGEWSLPRGNWLLPAHYELSPALIAKAIATRLEKSDLPTDVR 426

Query: 409  ERMAEISAMTTAQDPG------GVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASW 462
            ER+A   A+  A++         V+R P+FCSGCPHNTST+VPEGS+ALAGIGCH+MA W
Sbjct: 427  ERIAARVALIEAKEREAARPRISVERKPWFCSGCPHNTSTRVPEGSRALAGIGCHYMAMW 486

Query: 463  MGRNTESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYK 522
            M RNT++  QMGGEGV W G+  +TG  HVF NLG+GTYFHSG +A+R ++AA  NITYK
Sbjct: 487  MDRNTDTFSQMGGEGVAWTGQMHFTGEKHVFVNLGDGTYFHSGLLAVRASIAAKANITYK 546

Query: 523  ILFNDAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFH 582
            ILFNDAVAMTGGQPVDG +TV +IA Q+ AEG +++VV++DEPEKY G   + P  VT H
Sbjct: 547  ILFNDAVAMTGGQPVDGVLTVPQIAHQVLAEGASKIVVVTDEPEKY-GDGGMLPASVTVH 605

Query: 583  DRSELDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDC 642
             R +LD++Q +LRD  G T+LIYDQTCA EKRRRRKR    DPAKRAFIN  VCEGCGDC
Sbjct: 606  HRDQLDEIQVQLRDTAGVTILIYDQTCATEKRRRRKRGTMADPAKRAFINDAVCEGCGDC 665

Query: 643  SVQSNCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSV 702
            SV+SNCLSV P +T LG KRKI+QSSCNKDFSCVNGFCPSFVT EG Q+RK      G  
Sbjct: 666  SVKSNCLSVEPLETPLGTKRKINQSSCNKDFSCVNGFCPSFVTAEGAQVRKPAAAG-GKG 724

Query: 703  LTRKLADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQ 762
                 + +P P LP +   Y +LV GVGGTGVVT+G L+ MAAHLE +G +VLD  G AQ
Sbjct: 725  ALADFSALPQPALPTLERPYGVLVTGVGGTGVVTIGGLLGMAAHLEQKGVTVLDMAGLAQ 784

Query: 763  KGGTVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEA 822
            KGG V+S+V++AP+P  LH  RI+ G+A  VI CD +V++S + LS  R + T    N A
Sbjct: 785  KGGAVISHVQIAPTPAALHATRIATGEARLVIGCDAIVSASPEVLSKTRIDVTAAAINSA 844

Query: 823  ELPTADYV-----LFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVM 877
            + PTAD++      F  A  + D     L+ +VG D    +DAN  A KL+ D+++SN +
Sbjct: 845  DTPTADFIKNPNWKFPGASAEQD-----LRASVG-DACAFIDANAWAVKLLADSIYSNPL 898

Query: 878  MLGFAWQKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSA--VDPSAVTDLLDDSNA 935
            +LGFAWQKG +PL   +L++AIELNGVA+++N  AF WGR  A   + +    L     A
Sbjct: 899  LLGFAWQKGWVPLRRESLVRAIELNGVAVEKNLLAFDWGRYLAHHGEAALAAQLQITPRA 958

Query: 936  QVVEVKPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLG-ETNLLLTRAV 994
            QVV + PE TLD +I  R   L  YQN  +A +YR AV  VR AE+ +G    L L  AV
Sbjct: 959  QVVAM-PE-TLDSVIRQREALLTAYQNPAYAARYRAAVESVRAAEKRVGANPRLPLAEAV 1016

Query: 995  AQQLYRFMAYKDEYEVARLFAETDFMKEVNETFEG----DFKVHFHLAPPLLSGETDAQG 1050
            A+ L + MAYKDEYEVARL+A+  F+ ++   FEG    D+++ FHLAPPLL+ + D+ G
Sbjct: 1017 ARNLAKLMAYKDEYEVARLYADPAFLDKLRAQFEGEPGRDYQLSFHLAPPLLA-KRDSHG 1075

Query: 1051 RPKKRRFGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELN 1110
               KRRFGP M  AFRLLA+ +GLRGTA D F  +A+R+ +R +++DY ++ +  G  LN
Sbjct: 1076 HLVKRRFGPAMLTAFRLLARAKGLRGTAFDVFGKTAERRAERKLIEDYIAMAEEFGATLN 1135

Query: 1111 ASNYETFLQLAELPADVRGYGPVREQAAESIREKQTQLI 1149
            A   +T + LA LP D+RG+G V+E   E    ++  L+
Sbjct: 1136 ADRLDTAVALASLPDDIRGFGHVKEANMEKAAARRVALL 1174


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: 3132
Number of extensions: 124
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: 1186
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1139
Effective search space:  1281375
Effective search space used:  1281375
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)
SQLite3 databases

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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