Alignments for a candidate for iorAB in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Ruegeria conchae TW15

Align Indolepyruvate oxidoreductase (characterized, see rationale)
to candidate WP_010437962.1 G7G_RS0102470 indolepyruvate ferredoxin oxidoreductase family protein

Query= uniprot:I7EJ57
         (1140 letters)



>NCBI__GCF_000192475.1:WP_010437962.1
          Length = 1131

 Score = 1711 bits (4430), Expect = 0.0
 Identities = 847/1134 (74%), Positives = 950/1134 (83%), Gaps = 3/1134 (0%)

Query: 1    MTQLSHDFRSYQLDDRYDYTKGRVFLTGTQALARVMLDQARRDRSAGLNTAGFVSGYRGS 60
            M+ L  + R+YQLDDRY  T+GRVFLTGTQALAR+M+DQARRDR AGLNT+GFVSGYRGS
Sbjct: 1    MSHLDRNIRTYQLDDRYSLTQGRVFLTGTQALARIMMDQARRDRQAGLNTSGFVSGYRGS 60

Query: 61   PLGGVDLEFWRSRKRMDAHNITFMPAVNEDLGATAVLGAQQAILDPHCEVEGVFSMWYGK 120
            PLGG+DLE WR+++R+ A  ITFMPAVNEDLGATAVLGAQQA LDPHCEVEG+FSMWYGK
Sbjct: 61   PLGGLDLELWRAKERLIADRITFMPAVNEDLGATAVLGAQQATLDPHCEVEGIFSMWYGK 120

Query: 121  GPGVDRSGDALKHGNAYGSSEKGGVLVVAGDDHGCVSSSMPHQSDVAFMSWFMPVLNPAD 180
            GPGVDRSGDALKHGNAYGS+ KGGVLVVAGDDHGCVSSSMPHQSDVAFM+WFMP LNPA 
Sbjct: 121  GPGVDRSGDALKHGNAYGSAPKGGVLVVAGDDHGCVSSSMPHQSDVAFMAWFMPTLNPAS 180

Query: 181  VSEFLQFGEYGFALSRYSGTWVGFKAVSETVESARSVELRPDRSFTYPELPDYPGGLHIR 240
            V E+L+FGEYGFALSR+SGTWVGFKA+SETVESARSV+LRPDRSFT P +     GLH+R
Sbjct: 181  VEEYLEFGEYGFALSRFSGTWVGFKAISETVESARSVDLRPDRSFTLPRIDLPERGLHVR 240

Query: 241  RSDLPSPEIETRIHAKLRAVRAFAEANPIDTRIYDLPKAKFGFVTTGKGHLDLMEALRLL 300
             +DLPSPEIETRI  KLRAVRAFAE NPID RIYD+  AKFGFVTTGKGHLDLMEALRLL
Sbjct: 241  TADLPSPEIETRIQHKLRAVRAFAEENPIDRRIYDIDNAKFGFVTTGKGHLDLMEALRLL 300

Query: 301  GLDQAACKRLGIDIYKVGMVWPLARTEALRFVKGKQEVLVVEEKRGIIESQFKEYFYDWP 360
            GLD+AAC+RLGIDIYKVGMVWPLAR  ALRFVKGK EVLVVEEKRGIIESQFKEYFYDWP
Sbjct: 301  GLDEAACRRLGIDIYKVGMVWPLARRNALRFVKGKAEVLVVEEKRGIIESQFKEYFYDWP 360

Query: 361  GDKPERMVGKHDSQGNPLIPWTGELSPLTLVPIVAERLNRFFPEENLLDRANALTAQPPR 420
            GDKP +MVGK+DS G PLIPWTGELSPL L PIVA RL+ FFPEENL  +A ALT  PP 
Sbjct: 361  GDKPHKMVGKYDSHGEPLIPWTGELSPLMLAPIVAARLDTFFPEENLPAKARALTETPPP 420

Query: 421  LLNVPGATRTPYFCSGCPHNTSTKLPEGSKANSGIGCHVMASWMDRDTAGYAQMGGEGVP 480
             +NV GATRTPYFCSGCPHNTSTK+P+GS A SGIGCHVMASWMDR+T GYAQMGGEGVP
Sbjct: 421  EINVSGATRTPYFCSGCPHNTSTKVPDGSTAASGIGCHVMASWMDRETVGYAQMGGEGVP 480

Query: 481  WTVASKFNGGKHVFQNLGEGTWYHSGSLAIRQAVAADTNITYKILYNDAVAMTGGQPVDG 540
              VAS+FNGGKH+FQNLGEGTWYHSGSLAIRQAVAA TNITYKILYNDAVAMTGGQPVDG
Sbjct: 481  HVVASQFNGGKHIFQNLGEGTWYHSGSLAIRQAVAAGTNITYKILYNDAVAMTGGQPVDG 540

Query: 541  PVSVSGIAQTCRAEGVDRIALVSDDIEKFSKSEFPAGTSFHDRSDLDSVQRELREIPGVT 600
            PVSV+GIAQTCRAEGV+RIALVSDDI KF ++EFPAGT+FHDR+++DS+QRELR+IPGVT
Sbjct: 541  PVSVAGIAQTCRAEGVERIALVSDDITKFGRAEFPAGTTFHDRAEMDSLQRELRDIPGVT 600

Query: 601  VLIYEQTCATEKRRRRKRGTMEDPKRFAFINDLACEGCGDCSVESNCLSVEPKETPFGRK 660
            VLIYEQTCATEKRRRRKRG MEDP++F +INDL CEGCGDCSV SNCLSVEP+ETP GRK
Sbjct: 601  VLIYEQTCATEKRRRRKRGMMEDPQKFVWINDLVCEGCGDCSVASNCLSVEPRETPLGRK 660

Query: 661  RKINLSSCNKDFSCLNGFCPSFVTVEGATRRKKEVAALDASALTADLPSPALPSLKEPFD 720
            RKINLSSCNKDFSCLNGFCPSFVT+EGATRRK+ V  LD  AL A LP P+  SL  PFD
Sbjct: 661  RKINLSSCNKDFSCLNGFCPSFVTIEGATRRKQSV-DLDLDALEAGLPLPSAASLGSPFD 719

Query: 721  LLVTGVGGTGVVTVGALITMAAHLEGKGASVLDFTGFAQKFGTVLGYIRLSNTPEALHQV 780
            LLVTGVGGTGVVTVGALITMAAHLEGKGASVLDFTGFAQKFGTVL YIRL   P+ L+QV
Sbjct: 720  LLVTGVGGTGVVTVGALITMAAHLEGKGASVLDFTGFAQKFGTVLSYIRLGKEPDTLNQV 779

Query: 781  RIDQSAADAVIGCDVVVSSAPKASAHYRDGTKMVLNRAEMPTGDLVLRRDADLMANLRET 840
            RIDQ AADAVIGCDVVVSSAPKASAHY  GT++VLNRAEMPTGDLVL RDA L  + RE 
Sbjct: 780  RIDQGAADAVIGCDVVVSSAPKASAHYAPGTRVVLNRAEMPTGDLVLHRDAQLRVDAREQ 839

Query: 841  SIADVIGADNLSGFNANEAAETLLGDAVLANVMMLGFAWQNGLVPVSLGALDQAIVLNGV 900
            +IADV+GA+NL+  +AN  AE LLG  V ANV+MLG+AWQ  LVPVS  AL QAI+LNGV
Sbjct: 840  AIADVVGAENLTSLDANAMAEALLGGTVFANVIMLGYAWQKALVPVSHTALSQAILLNGV 899

Query: 901  AIEKNRLAFAIGRAFAHDPARLSDLYHEADAPEETLAELIDRRATFLTGYQDVAYAQSYT 960
            A++KNRLAFA+GR  A DP R+  L    +  E+TL +LI+RR  FLT YQD  YA  Y 
Sbjct: 900  AVKKNRLAFALGRCLAVDPERVQGLAQPTET-EDTLDQLIERRVAFLTDYQDAEYANRYA 958

Query: 961  ALLEVLRNALPSKGSDALVTAAARSLFKLMAYKDEFEVARLLSDDSFKHQLEAEFDGDFR 1020
              ++ LR++  S  SD LV   AR+LF+ MAYKDEFEVARL +   F  +L  +F+GD++
Sbjct: 959  QRIKALRSS-KSDISDRLVETIARNLFRFMAYKDEFEVARLQTSPDFSAELSQQFEGDYK 1017

Query: 1021 VNYHLAPPLLSRKSDARGRPQKMQFGAWMRPALRLLAKGRRMRGSRWNPFGRHEEARLHR 1080
              YH APPLLS + D R RP K+  GAWM P LR L++ R +RGS  NPFG H EARLHR
Sbjct: 1018 TKYHFAPPLLSWRKDERRRPVKIALGAWMHPVLRGLSRLRGLRGSPLNPFGYHAEARLHR 1077

Query: 1081 DLLAWYQTIITRTAEHYSHEHHDGWLKVLSAPMDIRGYGPVRMAAAEKVKAEVS 1134
            ++L W++ ++     + +      WL+  SA   IRG+GPVR  + E  +AEVS
Sbjct: 1078 NILNWFEELLNMYQTNPTARSEAEWLRAFSAADQIRGFGPVREESFETARAEVS 1131


Lambda     K      H
   0.319    0.135    0.406 

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: 3400
Number of extensions: 112
Number of successful extensions: 4
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: 1140
Length of database: 1131
Length adjustment: 46
Effective length of query: 1094
Effective length of database: 1085
Effective search space:  1186990
Effective search space used:  1186990
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 (21.8 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Sep 24 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