Alignments for a candidate for iorAB in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Paraburkholderia bryophila 376MFSha3.1

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate H281DRAFT_02122 H281DRAFT_02122 indolepyruvate ferredoxin oxidoreductase

Query= reanno::BFirm:BPHYT_RS02015
         (1195 letters)



>FitnessBrowser__Burk376:H281DRAFT_02122
          Length = 1195

 Score = 2266 bits (5872), Expect = 0.0
 Identities = 1127/1195 (94%), Positives = 1157/1195 (96%)

Query: 1    MTARLPIDGTPALADYKLSDNLTATRGRIFLTGTQALVRLVLMQRAADKARGMNTAGFIS 60
            MTARLPIDGTPAL+DYKLSDNLTATRGRIFLTGTQALVRL LMQR+ D+ARGMNTAGFIS
Sbjct: 1    MTARLPIDGTPALSDYKLSDNLTATRGRIFLTGTQALVRLALMQRSLDRARGMNTAGFIS 60

Query: 61   GYRGSPLGMVDQQLWKAKKLLAASDIRFLPAINEELGGTAVLGTQRVESDPERTVEGVFA 120
            GYRGSPLGMVDQQLWKAKKLL+ASDIRFLPAINEELGGTAVLGTQRVE+DPERTVEGVFA
Sbjct: 61   GYRGSPLGMVDQQLWKAKKLLSASDIRFLPAINEELGGTAVLGTQRVEADPERTVEGVFA 120

Query: 121  MWYGKGPGVDRAGDALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPV 180
            MWYGKGPGVDRAGDALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPV
Sbjct: 121  MWYGKGPGVDRAGDALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPV 180

Query: 181  VNPSNIADMLEFGLYGWELSRFSGAWVGYKAISETVESGSTVDLDALRTDWTMPQDFEVP 240
            VNPSNIADMLEFGLYGW LSRFSGAWVGYKAISETVESGSTVDLDALRTDW+ P+DFE P
Sbjct: 181  VNPSNIADMLEFGLYGWALSRFSGAWVGYKAISETVESGSTVDLDALRTDWSAPEDFEAP 240

Query: 241  AGGLHNRWPDLPSLTIESRMHAKLDAVRHFARVNSIDKWIAPSPHANVGIVTCGKAHLDL 300
            +GGLHNRWPDLPSLTIESRMHAKLDAVRHFA+ NSIDKWIAPSPHANVGIVTCGKAHLDL
Sbjct: 241  SGGLHNRWPDLPSLTIESRMHAKLDAVRHFAKTNSIDKWIAPSPHANVGIVTCGKAHLDL 300

Query: 301  METLRRLDLTVADLEAAGVRIYKVGLSFPLEMTRIDAFVSGLSEVLVIEEKGPVIEQQIK 360
            METLRRLDLTVADL+AAGVRIYKVGLSFPLEM RID FV GLSEVLVIEEKGPVIEQQIK
Sbjct: 301  METLRRLDLTVADLDAAGVRIYKVGLSFPLEMMRIDTFVEGLSEVLVIEEKGPVIEQQIK 360

Query: 361  DYLYNRTQGTRPIVVGKNAEDGTLLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVD 420
            DYLYNRTQG RP V+GK A+DG++LLSSLGELRPSRILPVFANWLAKHKPALDRRERVVD
Sbjct: 361  DYLYNRTQGARPAVIGKQAQDGSMLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVD 420

Query: 421  LVAPQILSNAADSVKRTPYFCSGCPHNTSTKVPEGSIAHAGIGCHFMASWMERDTTGLIQ 480
            LVAPQILSNAADSVKRTPYFCSGCPHNTSTKVPEGSIAHAGIGCHFMASWMERDTTGLIQ
Sbjct: 421  LVAPQILSNAADSVKRTPYFCSGCPHNTSTKVPEGSIAHAGIGCHFMASWMERDTTGLIQ 480

Query: 481  MGGEGVDWASHSMFTKTRHVFQNLGDGTYFHSGILAIRQAVAAKATITYKILYNDAVAMT 540
            MGGEGVDWASHSMFTKTRHVFQNLGDGTYFHSGILAIRQAVAAKATITYKILYNDAVAMT
Sbjct: 481  MGGEGVDWASHSMFTKTRHVFQNLGDGTYFHSGILAIRQAVAAKATITYKILYNDAVAMT 540

Query: 541  GGQPVDGSISVPQIARQVEAEGVSRFVVVSDEPEKYDGHHDQFPKGTTFHHRSEMDTVQR 600
            GGQPVDGSISVPQIARQVEAEGVSRFVVVSDEPEKYDGHHD FPKGTTFHHRSEMDTVQR
Sbjct: 541  GGQPVDGSISVPQIARQVEAEGVSRFVVVSDEPEKYDGHHDLFPKGTTFHHRSEMDTVQR 600

Query: 601  QLRDTDGVTVLIYDQTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVE 660
            +LRDTDGVTVLIYDQTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVE
Sbjct: 601  ELRDTDGVTVLIYDQTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVE 660

Query: 661  PVETALGRKRRIDQSSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALAARVEALP 720
            PVETALGRKRRIDQSSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALA R+ AL 
Sbjct: 661  PVETALGRKRRIDQSSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALAERINALR 720

Query: 721  IPATHLDAAPYDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFV 780
            +PAT LDAAPYDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFV
Sbjct: 721  LPATQLDAAPYDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFV 780

Query: 781  RFAARDEWLNQVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVT 840
            RFAARDEWLNQVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFV 
Sbjct: 781  RFAARDEWLNQVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVQ 840

Query: 841  NPDATLHADALLDKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVS 900
            NPDATLHADAL+DKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVS
Sbjct: 841  NPDATLHADALIDKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVS 900

Query: 901  FGAMMRAIELNNVAVQMNQLAFSIGRLAAEDPAALEALWQARHLAKQSVRVDTLDELIAH 960
            FGA+MRAIELNNVAVQMNQLAFSIGRLAAEDPAALE+LWQARH AKQ+VR+DTLDELIAH
Sbjct: 901  FGALMRAIELNNVAVQMNQLAFSIGRLAAEDPAALESLWQARHAAKQTVRIDTLDELIAH 960

Query: 961  REGRLQTYGGASYVKRYRALVDAARRAETSVDAKSERVTRAVATTFYRLLAVKDEYEVAR 1020
            REGRLQ YGGASYVKRYRALVDAARRAE+++ A SERVTRAVATTFYRLLAVKDEYEVAR
Sbjct: 961  REGRLQIYGGASYVKRYRALVDAARRAESAIGANSERVTRAVATTFYRLLAVKDEYEVAR 1020

Query: 1021 LHTDAVFREALEAQFEGVAGKDFGIKFNLAPPTLTRPEPGKNPVKKTFGQWMWPVLGTLA 1080
            LHTDA FREALEAQFEGVAGKDFGI FNLAPP LTR   G NP KKTFGQWMWPVLG LA
Sbjct: 1021 LHTDAAFREALEAQFEGVAGKDFGINFNLAPPALTRAHSGANPTKKTFGQWMWPVLGVLA 1080

Query: 1081 KFSSLRGTMLDPFGRTLERKMERELAGDYETTLQRALARLDAGNLEDVAKLADLHARVRG 1140
            K   LRGTMLDPFGRTLERKME ELA DYETTLQRALA+L+A NL+DVAKLADLHARVRG
Sbjct: 1081 KVRGLRGTMLDPFGRTLERKMEHELADDYETTLQRALAKLNADNLDDVAKLADLHARVRG 1140

Query: 1141 YGHVKLANLAGVKRGERDLAARLQIEAATGESVRKSLEEMKGAGQLRGIPVVVAK 1195
            YGHVKLANLAGVKRGERDLAARLQIEAATG SV+KSLEE+KGAGQLRGIPVVVAK
Sbjct: 1141 YGHVKLANLAGVKRGERDLAARLQIEAATGTSVKKSLEEVKGAGQLRGIPVVVAK 1195


Lambda     K      H
   0.319    0.134    0.399 

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: 3772
Number of extensions: 93
Number of successful extensions: 1
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: 1195
Length of database: 1195
Length adjustment: 47
Effective length of query: 1148
Effective length of database: 1148
Effective search space:  1317904
Effective search space used:  1317904
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: 59 (27.3 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