Alignments for a candidate for iorAB in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Xanthobacter autotrophicus Py2

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_011996048.1 XAUT_RS01975 MFS transporter

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



>NCBI__GCF_000017645.1:WP_011996048.1
          Length = 1159

 Score = 1062 bits (2747), Expect = 0.0
 Identities = 563/1158 (48%), Positives = 741/1158 (63%), Gaps = 16/1158 (1%)

Query: 12   ALADYKLSDNLTATRGRIFLTGTQALVRLVLMQRAADKARGMNTAGFISGYRGSPLGMVD 71
            AL    L D    T+ R+F++GTQALVRL LMQ+  D+  G+NTAG+++GYRGSPLG +D
Sbjct: 2    ALTPVSLDDKYDLTQDRVFVSGTQALVRLALMQKERDRRAGLNTAGYVTGYRGSPLGGLD 61

Query: 72   QQLWKAKKLLAASDIRFLPAINEELGGTAVLGTQRVESDPERTVEGVFAMWYGKGPGVDR 131
            QQ  +A+K+L A+DI+F   +NE+L  TA+ G+Q+ E   E   +GVF +WYGKGPGVDR
Sbjct: 62   QQFLRAEKILKANDIKFQSGLNEDLAATALWGSQQAELRGEGRFDGVFGLWYGKGPGVDR 121

Query: 132  AGDALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPVVNPSNIADMLE 191
            +GD  +H N  G+S HGGVL + GDDH C SS+  HQS+F  +   +PV+NP+ + ++++
Sbjct: 122  SGDVFRHANNAGTSRHGGVLALMGDDHTCESSTTAHQSEFHFVDVMIPVLNPAGVQEIID 181

Query: 192  FGLYGWELSRFSGAWVGYKAISETVESGSTVDLDALRTDWTMPQDFEVPAGGLHNRWPDL 251
            +GLYGW LSRFSGAWVG KA+ +T+ES   VD    R        F +P GGL+ R  D 
Sbjct: 182  YGLYGWALSRFSGAWVGLKAVKDTIESTGIVDGRLERVRIEPALGFAMPPGGLNIRLGDT 241

Query: 252  PSLTIESRMHAKLDAVRHFARVNSIDKWI-APSPHANVGIVTCGKAHLDLMETLRRLDLT 310
            P    E     K DAV HF R N ++++I +      +GI T GK++LD+   L  L + 
Sbjct: 242  PLAQEERLQEFKRDAVLHFLRANRLNRFITSGGSRPRIGIATVGKSYLDVRLALDELGID 301

Query: 311  VADLEAAGVRIYKVGLSFPLEMTRIDAFVSGLSEVLVIEEKGPVIEQQIKDYLYNRTQGT 370
                   G+RI+KV   +PLE   +  F  GL  ++V+EEK  +IE Q+++ LY      
Sbjct: 302  EVRANDLGLRIWKVACPWPLETEGLKEFARGLDLIMVVEEKRSLIEVQVREELYG--TAN 359

Query: 371  RPIVVGKNAEDGTLLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVDL-VAPQILSN 429
            +P+ +GK  E+G  L    G L P+ I       L  +    D  ERV +L  A ++L+ 
Sbjct: 360  QPVCIGKKDEEGRWLFPVKGSLDPNDIAIQLGRRLLAYGNIPDIAERVAELEEAQRVLAA 419

Query: 430  AADSVKRTPYFCSGCPHNTSTKVPEGSIAHAGIGCHFMASWMERDTTGLIQMGGEGVDWA 489
             +D   R PYFCSGCPHN+STKVPEG  A+AGIGCH+M  WM+R+TTG  QMGGEG +W 
Sbjct: 420  TSDVATRIPYFCSGCPHNSSTKVPEGMRAYAGIGCHYMVQWMDRETTGFTQMGGEGANWI 479

Query: 490  SHSMFTKTRHVFQNLGDGTYFHSGILAIRQAVAAKATITYKILYNDAVAMTGGQPVDGSI 549
              S F+K  HVFQNLGDGTY HSG LA+R A AAK  +TYKIL+NDAVAMTGGQ  DG +
Sbjct: 480  GESSFSKRPHVFQNLGDGTYNHSGYLALRAACAAKVNVTYKILFNDAVAMTGGQKHDGDL 539

Query: 550  SVPQIARQVEAEGVSRFVVVSDEPEKYDGHHDQFPKGTTFHHRSEMDTVQRQLRDTDGVT 609
            +VP IARQV AEGV R VVV+DEP+KY   +  +P G T HHR E+++VQR+L +  GVT
Sbjct: 540  TVPVIARQVAAEGVERVVVVTDEPDKY-APNTHWPTGLTIHHRDELESVQRELAEIPGVT 598

Query: 610  VLIYDQTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVEPVETALGRK 669
            VLIYDQTCA+EKRRRRK+G++PDPDKR+ INE VCEGCGDCGV+SNC+SV+P+ET  GRK
Sbjct: 599  VLIYDQTCASEKRRRRKRGQYPDPDKRVLINERVCEGCGDCGVKSNCVSVQPLETEWGRK 658

Query: 670  RRIDQSSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALAARVEALPIPATHLDAA 729
            R IDQSSCNKD+SCVNGFCPSFVTV+G K KK AGAA           ALP PA      
Sbjct: 659  REIDQSSCNKDFSCVNGFCPSFVTVKGAKPKKVAGAA----GAEGDWPALPEPAHPEIHG 714

Query: 730  PYDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARDEWL 789
             Y I+ TGVGGTGVVT+GA++ MAAHLEGK+  ++D  G AQKGG+V S +R A     +
Sbjct: 715  TYGIIATGVGGTGVVTIGAILGMAAHLEGKACGMIDMAGLAQKGGAVYSHIRLANDPADI 774

Query: 790  NQVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVTNPDATLHAD 849
              +R+  + ADV+L  D+VV  +   L  V+ G+T +VVNTH +    F  N D +L  +
Sbjct: 775  TAIRVPARGADVVLGGDLVVAGTKKVLAAVKPGKTIVVVNTHEVLPGDFTRNADYSLPTE 834

Query: 850  ALLDKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVSFGAMMRAIE 909
             +   +R  AG+E     +A  LA    G+ +  NI M+GYA+Q G +P+S  A+ RAIE
Sbjct: 835  RIKRTIRDLAGSEMTHFIEASRLAQALFGNALAQNIFMVGYAYQFGALPLSAEAIERAIE 894

Query: 910  LNNVAVQMNQLAFSIGRLAAEDPAALEALWQAR-HLAKQSVRVD-TLDELIAHREGRLQT 967
            LN  AV MN+ AF  GR AA DPAA+E +   +  +A  + R+  +LDE+IA R   L  
Sbjct: 895  LNGEAVAMNKTAFLWGRRAAHDPAAVEKVATPKGEIASDARRLSASLDEVIARRVAELTA 954

Query: 968  YGGASYVKRYRALVDAARRAETSVDAKSERVTRAVATTFYRLLAVKDEYEVARLHTDAVF 1027
            Y  A+Y +RY  LV+  R AE         +  AVA + ++L+A KDEYEV+RL+ D  F
Sbjct: 955  YQDAAYGQRYARLVEKVRAAEAQKAPGRGGLAEAVAKSLFKLMAYKDEYEVSRLYADGAF 1014

Query: 1028 REALEAQFEGVAGKDFGIKFNLAPPTLTRPEP-GKNPVKKTFGQWMWPVLGTLAKFSSLR 1086
            R    A F+G    D   +F+LAPP L R +P    P K T G WM    G LAK   LR
Sbjct: 1015 RAQAAAAFDG----DLTFEFHLAPPLLARHDPITGEPRKMTLGPWMMRAFGLLAKLKGLR 1070

Query: 1087 GTMLDPFGRTLERKMERELAGDYETTLQRALARLDAGNLEDVAKLADLHARVRGYGHVKL 1146
            GT+ DPFG T ER+ ER L G YE T++  +A LD  +      +A L  ++RG+GHVK 
Sbjct: 1071 GTVFDPFGYTAERRTERALIGAYEKTVEELIAGLDGASHAVAVAVAALPEKIRGFGHVKA 1130

Query: 1147 ANLAGVKRGERDLAARLQ 1164
             +LA V+  E +L AR +
Sbjct: 1131 RHLAAVQAEEAELLARFR 1148


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: 3087
Number of extensions: 114
Number of successful extensions: 11
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: 1159
Length adjustment: 47
Effective length of query: 1148
Effective length of database: 1112
Effective search space:  1276576
Effective search space used:  1276576
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