Alignments for a candidate for iorAB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Herbaspirillum seropedicae SmR1

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate HSERO_RS21380 HSERO_RS21380 MFS transporter

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



>FitnessBrowser__HerbieS:HSERO_RS21380
          Length = 1199

 Score = 1126 bits (2912), Expect = 0.0
 Identities = 585/1174 (49%), Positives = 776/1174 (66%), Gaps = 36/1174 (3%)

Query: 8    LDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQ 67
            LDD  L+D+Y  E GRVF+TG QALVR+P++Q   D++ GLNTAG ++GYRGSPLGAVDQ
Sbjct: 13   LDDVSLDDKYTLERGRVFMTGIQALVRLPMLQRQYDQRAGLNTAGFITGYRGSPLGAVDQ 72

Query: 68   ALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRA 127
               +A+  L+  +I F P +NEDLAAT + GTQQV   +  Q +GVF LWYGKGPGVDR 
Sbjct: 73   TAEKARKYLEAKQIKFHPGMNEDLAATSVWGTQQVNLFKGAQYDGVFSLWYGKGPGVDRC 132

Query: 128  GDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEF 187
            GD  KH    G+S HGGVLV+AGDDH   SS+  HQS+    +  +P + P+++ EYL++
Sbjct: 133  GDVFKHANMAGTSRHGGVLVIAGDDHAAKSSTAAHQSEHILKACGIPVLYPSSVQEYLDY 192

Query: 188  GLWGYALSRYSGCWVGFKAISETVESAASVEI-PPAPDFVTPDDFTAPESGLHYRWPDLP 246
            GL G+A+SRY+G WV  K +++ VES  SV I P       P DF  P  GL+ R PD  
Sbjct: 193  GLHGWAMSRYTGLWVAMKCVTDLVESGMSVMIDPERVQIQLPADFELPPDGLNIRQPDTV 252

Query: 247  GPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDED 306
              Q    I +K  A  A+ARAN+++R ++D+  AR GI+T GK +LD  +AL+ LGIDE 
Sbjct: 253  LGQEARMINYKWYAALAYARANKLNRIIWDSPRARIGIITAGKSYLDTRQALEDLGIDEQ 312

Query: 307  KARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEV 366
             ARD+G+ +YKVGM WPLE  G+ +F  G +E+LV+EEKR I+E Q+KE +         
Sbjct: 313  AARDIGIRLYKVGMTWPLEAEGVREFAQGLDEILVVEEKRQILEYQLKEELYNWRDDVRP 372

Query: 367  LITGKQDEL-----------GRPLIPYVGELSPKLVAGFLAARLGRFF-----EVDFSER 410
             + GK D+            G  L+P   EL+P  +A  +A R+ R+F     E     R
Sbjct: 373  RVVGKFDDTGEWSGSQREGHGNWLLPATYELNPAQIARAIATRISRYFAGHPVEQQVRAR 432

Query: 411  MAEISA------MTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMG 464
            +A + A      +++  DP    R+P+FCSGCPHNTSTK+PEGS+ LAGIGCH+M +WM 
Sbjct: 433  VAYLEAKEATLNISSKPDP-DKDRIPHFCSGCPHNTSTKLPEGSRGLAGIGCHYMVTWMD 491

Query: 465  RNTESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKIL 524
            R T+    MGGEGV W+G++ +T   HVF NLG+GTYFHSG +A+R +VAA +NITYKIL
Sbjct: 492  RETKLFTHMGGEGVTWVGQAPFTDEKHVFANLGDGTYFHSGLLAVRASVAAKVNITYKIL 551

Query: 525  FNDAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDR 584
            +NDAVAMTGGQ  DG +    I++Q+AAE V  ++V++DEP+KY      + + VT   R
Sbjct: 552  YNDAVAMTGGQEFDGPLDPAMISRQLAAENVRPIIVVTDEPDKYPVGTQ-WAEGVTIRHR 610

Query: 585  SELDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSV 644
            SELD VQRELR+ PG + +IYDQTCA+EKRRRRKR  +PDPAKRA IN  VCEGCGDCSV
Sbjct: 611  SELDAVQRELREQPGVSAMIYDQTCASEKRRRRKRNAYPDPAKRAVINEAVCEGCGDCSV 670

Query: 645  QSNCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRK--SRGVDTGSV 702
            QSNCLSV P +TE GRKR+I+QSSCNKD+SCVNGFCPSFVT+EGGQL+K      D G  
Sbjct: 671  QSNCLSVEPLETEFGRKRQINQSSCNKDYSCVNGFCPSFVTVEGGQLKKPARAQADVGPA 730

Query: 703  LTRKLADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQ 762
                L  +P P LP +   Y +LV GVGGTGV+T+GQ+I MAAH+E R  SVLD  G AQ
Sbjct: 731  ----LPSLPEPVLPGLAQPYGILVTGVGGTGVITIGQIIAMAAHVEGRACSVLDMSGLAQ 786

Query: 763  KGGTVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEA 822
            KGG V+S+VR+A     +H  R+  G AD VI CD++V +S+ ALS +    T    N  
Sbjct: 787  KGGPVMSHVRVAEDAAHIHSTRVGTGMADLVIGCDVIVTASRDALSRMGEGRTHAAVNST 846

Query: 823  ELPTADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFA 882
            ++PTA +V   D         G +  A G D+   +DA  IA  LMGD + +N+ MLG+A
Sbjct: 847  QMPTAAFVRNPDWQFPTASSEGEIARACGRDNLSLVDAGRIATALMGDAIATNMFMLGYA 906

Query: 883  WQKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLL--DDSNAQVVEV 940
            WQKG +PLSEAAL++AIELN + ++ NK+AF WGR +A D + V      +  +AQV+E 
Sbjct: 907  WQKGWVPLSEAALLRAIELNALQVEFNKQAFAWGRAAAHDVAFVLAAAGRNGMSAQVIEF 966

Query: 941  KPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGET--NLLLTRAVAQQL 998
            K  PTLDEL+  R   L +Y N  +A  YRD V  VR  E +LGE    L L+RAVA  L
Sbjct: 967  KRTPTLDELVERRVAFLTDYLNAAYARSYRDFVEQVRARESALGEAGRGLKLSRAVASYL 1026

Query: 999  YRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFG 1058
            ++ MAYKDEYEVARL A+  F  ++   FEGD+K+ FHLAPPLL+ + D +G  +K+ FG
Sbjct: 1027 FKLMAYKDEYEVARLHADPAFRAKIAGMFEGDYKLRFHLAPPLLA-KRDDKGHLRKQAFG 1085

Query: 1059 PWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFL 1118
             WM   F +LA+LR LRGTA+DPF Y+ +R+ +RA++ +Y++ + R+   L   N E   
Sbjct: 1086 SWMMPVFGVLARLRFLRGTALDPFAYTEERRQERALITEYRATLSRLLDRLTPENLEQIT 1145

Query: 1119 QLAELPADVRGYGPVREQAAESIREKQTQLIKAL 1152
             +A +P ++RGYG V+E+  ++  EKQ  L+  L
Sbjct: 1146 AVARIPEEIRGYGHVKERHLKAAMEKQAALLAQL 1179


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: 3104
Number of extensions: 124
Number of successful extensions: 9
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: 1199
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1152
Effective search space:  1296000
Effective search space used:  1296000
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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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 2024 update 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