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_RS19540 RR42_RS19540 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Cup4G11:RR42_RS19540
          Length = 1197

 Score = 1124 bits (2907), Expect = 0.0
 Identities = 590/1175 (50%), Positives = 793/1175 (67%), Gaps = 38/1175 (3%)

Query: 8    LDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQ 67
            L +  LED+Y  E GRV+++GTQALVR+P++Q   DR  GLNTAG +SGYRGSPLGA+DQ
Sbjct: 17   LANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQ 76

Query: 68   ALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRA 127
            +LW+AK  L  + I F   +NEDLAAT + G+QQV    D + EGVFG+WYGKGPGVDR 
Sbjct: 77   SLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRT 136

Query: 128  GDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEF 187
             D  KH  + GSS HGGVLV+AGDDH   SS++ HQS+  F +  +P + P+N+ EYL++
Sbjct: 137  SDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDY 196

Query: 188  GLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLHYRWPDLP 246
            GL  +A+SRYSG WV  K +++ VES+ASVE+ P   + V P DF  P  GL+ RWPD P
Sbjct: 197  GLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPP 256

Query: 247  GPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDED 306
              Q    +++K  A  A+ RAN+IDR   D+  ARFGI+T GK +LD  +AL  LG+D++
Sbjct: 257  LEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDE 316

Query: 307  KARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEV 366
                +G+ +YKVG VWPLE  G   F  G +E+LV+EEKR I+E  +KE +         
Sbjct: 317  TCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRP 376

Query: 367  LITGKQDELGRP-----------LIPYVGELSPKLVAGFLAARLGRF-FEVDFSERMAEI 414
             + GK DE               L+P   ELSP ++A  +A RL +F    D   R+A  
Sbjct: 377  KVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIAAR 436

Query: 415  SAMTTAQDPG------GVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTE 468
             A+  A++          +R P+FCSGCPHNTST VPEGS+ALAGIGCH+M  WM R+T 
Sbjct: 437  IAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTS 496

Query: 469  SLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDA 528
            +  QMGGEGV WIG++ + G+ HVF NLG+GTYFHSG +AIR ++AAG+NITYKIL+NDA
Sbjct: 497  TFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDA 556

Query: 529  VAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELD 588
            VAMTGGQP+DG+++V  +A Q+AAEG  ++VV++DEPEKY     L P+ V  H R ELD
Sbjct: 557  VAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKL-PQGVEVHHRDELD 615

Query: 589  QVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNC 648
            ++QRELR++PG T+LIYDQTCA EKRRRRKR  +PDPAKRAFIN  VCEGCGDCSV+SNC
Sbjct: 616  RIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNC 675

Query: 649  LSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLA 708
            LSV P +TELG KR+I+QSSCNKDFSCVNGFCPSFVT EG Q++K    +   V    L 
Sbjct: 676  LSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKP---ERHGVSMDNLP 732

Query: 709  DIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVL 768
             +P P LP +   Y +LV GVGGTGVVT+G L+ MAAHLE++G +VLD  G AQKGG VL
Sbjct: 733  ALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVL 792

Query: 769  SYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTAD 828
            S+V++A  PD+LH  RI+ G+AD VI CD +V++    +S  +   TR + N A+ PTA+
Sbjct: 793  SHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAE 852

Query: 829  YVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLL 888
            ++               ++NAVGE   D ++A+G+A  L+GD +F+N ++LG+AWQKG L
Sbjct: 853  FIKNPKWQFPGLSAEQDVRNAVGE-ACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWL 911

Query: 889  PLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDD--SNAQVVEVKPEPT- 945
            PLS  AL++AIELNG A+++NK AF WGR  A DP  V  L     + A+  EV   PT 
Sbjct: 912  PLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTS 971

Query: 946  ----LDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESL--GETNLLLTRAVAQQLY 999
                L++LI  R +HL  YQ+  +A  +RD V+ VR AE +L      L LT A A+ L 
Sbjct: 972  SGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLS 1031

Query: 1000 RFMAYKDEYEVARLFAETDFMKEVNETFEG----DFKVHFHLAPPLLSGETDAQGRPKKR 1055
            + MAYKDEYEVARL+ +  F+ ++   FEG    D++++F LAPPL++ + D +G   KR
Sbjct: 1032 KLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMA-KRDEKGHLVKR 1090

Query: 1056 RFGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYE 1115
            RFGP   + F +LAKL+GLRG   D F  +A+R+ +RA++ +Y++L++ + R L+A+N+ 
Sbjct: 1091 RFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHA 1150

Query: 1116 TFLQLAELPADVRGYGPVREQAAESIREKQTQLIK 1150
            T + LA LP D+RG+G V++     +R + T L++
Sbjct: 1151 TAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLE 1185


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: 3076
Number of extensions: 124
Number of successful extensions: 12
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: 1197
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1150
Effective search space:  1293750
Effective search space used:  1293750
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