Alignments for a candidate for iorAB in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Sulfuritalea hydrogenivorans DSM 22779

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_041097026.1 SUTH_RS03175 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000828635.1:WP_041097026.1
          Length = 1155

 Score = 1124 bits (2908), Expect = 0.0
 Identities = 582/1146 (50%), Positives = 770/1146 (67%), Gaps = 17/1146 (1%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            LED+Y   SGRVFLTGTQALVR+ L+Q   D   GLNTAG VSGYRGSPLG +DQALW+A
Sbjct: 10   LEDKYALASGRVFLTGTQALVRLLLLQRQRDALAGLNTAGYVSGYRGSPLGGLDQALWKA 69

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
            +  L ++ + F P +NEDLAAT L GTQQV      + +GVFG+WYGKGPGVDR GD  K
Sbjct: 70   RPHLAQSHVVFQPGVNEDLAATALWGTQQVNLSPGAKHDGVFGMWYGKGPGVDRCGDVFK 129

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            H  + G+  HGG+L VAGDDH   SS++ HQS+ AF +  MP + PA + +YL+ GL G+
Sbjct: 130  HANSAGTWKHGGILAVAGDDHAARSSTVAHQSEHAFKAAMMPVLVPAGVQDYLDLGLHGW 189

Query: 193  ALSRYSGCWVGFKAISETVESAASVEI-PPAPDFVTPDDFTAPESGLHYRWPDLPGPQLE 251
            A+SRYSGCWVGFKA+++TVES+ASV+I P     V PDD+  P  GL+ RWPD    Q  
Sbjct: 190  AMSRYSGCWVGFKAVADTVESSASVDISPDRVRIVLPDDYALPAGGLNIRWPDDRLLQEA 249

Query: 252  TRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDEDKARDM 311
              ++HKL A  A+ RAN++++ + D    R GI+TTGK +LD+ +A D LGID+  A ++
Sbjct: 250  RLLDHKLYAALAYCRANKLNQVVIDAPNPRLGIITTGKSYLDVRQAFDDLGIDDALAAEI 309

Query: 312  GLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEVLITGK 371
            G+ +YKVGMVWPLE  G+  F  G EE+LV+EEKR +IE Q+KE +          + GK
Sbjct: 310  GIRLYKVGMVWPLESDGVRRFAEGLEEILVVEEKRQLIEYQLKEELYNWREDVRPRVIGK 369

Query: 372  QDEL-------GRPLIPYVGELSPKLVAGFLAARLGRFF-EVDFSERMAEISAMTTAQDP 423
             DE        GR L+P  GELSP  +A  +A R+GR F      ER+A I A   +  P
Sbjct: 370  FDEKGEWALPNGRWLLPASGELSPAQIARVIADRIGRHFTSPRIRERLAIIEAKERSAAP 429

Query: 424  G-GVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNWIG 482
               V R PYFC GCPHNTST VPEGS+ALAGIGCHFM  WM R+T +   MGGEG  W+G
Sbjct: 430  AIQVARTPYFCPGCPHNTSTCVPEGSRALAGIGCHFMVLWMNRSTATYSHMGGEGAAWMG 489

Query: 483  KSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQIT 542
            ++ +T   HVF NLG+GTYFHSGS+AIR AVA+G+N TYKIL+NDAVAMTGGQPVDG +T
Sbjct: 490  QAPFTEQRHVFVNLGDGTYFHSGSLAIRAAVASGVNATYKILYNDAVAMTGGQPVDGNLT 549

Query: 543  VDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCTV 602
            V +IA Q+ AEGV+ VVV++D   +  GH DL P  V    R ELD +QRE+R+ PG + 
Sbjct: 550  VPQIAHQLHAEGVHHVVVVTDGTARAYGHPDL-PHGVPIRHRDELDAIQREMRECPGVSA 608

Query: 603  LIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRKR 662
            +IYDQTCAAEKRRRRKR +  DP +R FIN  VCEGCGDC VQSNCL+VVP +TE GRKR
Sbjct: 609  IIYDQTCAAEKRRRRKRGKMIDPPRRLFINEAVCEGCGDCGVQSNCLAVVPVETEFGRKR 668

Query: 663  KIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGSY 722
             IDQS+CNKD+SC  GFCPSFV++ GG ++K RG+   +     +A  PAP L      Y
Sbjct: 669  AIDQSACNKDYSCEKGFCPSFVSVLGGGVKKGRGLAGSTNGGDFIAVPPAPTLASTADPY 728

Query: 723  DLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLHQ 782
             +L+ GVGGTGVVT+G LI MAAH++ +G +VLD  G AQKGG V S+VR+   P+ +H 
Sbjct: 729  GILITGVGGTGVVTIGALIGMAAHIDGKGVTVLDMTGLAQKGGAVFSHVRICDDPEAIHA 788

Query: 783  VRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKADKR 842
            VR++ G+ADAVI  D++V +S  AL+ ++   TR+V N AE PTAD+    D      + 
Sbjct: 789  VRVATGEADAVIGGDVIVTASPDALTRMQSGRTRVVVNCAETPTADFTRNPDWQFPLARM 848

Query: 843  LGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIELN 902
              ++   VG      +DA+ +A +L+GD++ SN+ +LG+AWQ+GL+P+S  A+ +AIELN
Sbjct: 849  QAVVGETVGAGAAHFVDASDLAVRLLGDSIASNLFLLGYAWQQGLVPVSWDAIDRAIELN 908

Query: 903  GVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNYQN 962
            G A+  ++ AF WGR +A DP+ V           + V P PTLDELI  R + L  YQ+
Sbjct: 909  GTAVPLSRAAFLWGRRAAHDPAGVAAYARPK----IAVPPAPTLDELIAKRVRFLTEYQD 964

Query: 963  QRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFMKE 1022
              +A++YR  V  +R AE  +  +   LT  VA  L++ MA KDEYEVARL+AETDF+++
Sbjct: 965  AAYAERYRTQVEKIRTAEAFIDSSQ--LTETVAHNLFKLMAIKDEYEVARLYAETDFLQK 1022

Query: 1023 VNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAIDPF 1082
            + E FEGD+ + FHLAPPLL+      G+ KK  FGPWM   F+ LAK R  RG+  D F
Sbjct: 1023 IGERFEGDYTLQFHLAPPLLARPDPKTGKVKKLAFGPWMLTGFKWLAKARRYRGSRWDVF 1082

Query: 1083 RYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAESIR 1142
              SA+R+L+R++L DY++ + R+  +L+ +     + LA LP  +RG+G V+ +  ++  
Sbjct: 1083 GRSAERQLERSLLADYEADLARMAGKLDRTTLGDAIALANLPEKIRGFGHVKRRNIDAAM 1142

Query: 1143 EKQTQL 1148
             ++  L
Sbjct: 1143 PERDAL 1148


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: 3215
Number of extensions: 141
Number of successful extensions: 8
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: 1155
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1108
Effective search space:  1246500
Effective search space used:  1246500
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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