Alignments for a candidate for ofo in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Herbaspirillum autotrophicum IAM 14942

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_083438777.1 AKL27_RS01445 indolepyruvate ferredoxin oxidoreductase

Query= reanno::Cup4G11:RR42_RS19540
         (1197 letters)



>NCBI__GCF_001189915.1:WP_083438777.1
          Length = 1208

 Score = 1314 bits (3400), Expect = 0.0
 Identities = 686/1197 (57%), Positives = 850/1197 (71%), Gaps = 41/1197 (3%)

Query: 2    NAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAG 61
            +AP   P S      LANVSL+DKYT   G +++SG QALVRLP+LQ+ RDR AGLNTAG
Sbjct: 32   HAPSIAPAS------LANVSLDDKYTATSGLIFLSGIQALVRLPLLQQIRDRQAGLNTAG 85

Query: 62   FISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEG 121
            FISGYRGSPLG LD++LWKA++HL AH + FQ G NED+AAT+VWG+QQV++   A+++G
Sbjct: 86   FISGYRGSPLGGLDEALWKAQKHLDAHQVKFQPGTNEDMAATAVWGTQQVDLIGPAKYDG 145

Query: 122  VFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACG 181
            VF MWYGKGPGVDR  DV KH N AG+S  GGVL++AGDDH A SSTL HQS+HIF A  
Sbjct: 146  VFAMWYGKGPGVDRCGDVLKHMNHAGTSAKGGVLLVAGDDHGAYSSTLPHQSDHIFSASM 205

Query: 182  LPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDF 241
            +P+LYP NVQEYLD GLH WAMSR+SG  V  K + D VESSASV+ DP RVEI  P DF
Sbjct: 206  IPMLYPCNVQEYLDLGLHGWAMSRFSGCTVGFKALADTVESSASVDADPFRVEIKYPPDF 265

Query: 242  ILPPGGLNIRWPDPPL-----EQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMT 296
            ++P GGLN R     L     +QEA + DYK YA LAY RANK++R+ IDSP AR GI+ 
Sbjct: 266  VMPEGGLNARLSTDTLGVQARKQEALMQDYKIYAALAYARANKLNRVMIDSPKARLGIIA 325

Query: 297  GGKAYLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKR 356
             GK+YLD  +AL+ LG+D+   A IG+RL+KV   WPLE  G R FA+GL EILVVEEKR
Sbjct: 326  SGKSYLDVLEALSELGIDESFAADIGLRLFKVAMPWPLEPEGVREFAQGLDEILVVEEKR 385

Query: 357  QIMEYALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAI 416
            Q++EY LKE+LYNWRDDVRP+V GKFDEK    GEW  P+  WLL +  + S A IAR I
Sbjct: 386  QMVEYQLKEQLYNWRDDVRPRVIGKFDEK----GEWVAPRGEWLLTSKADFSVAQIARVI 441

Query: 417  ATRLDKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGS 476
            A R+ +F   +D+   I AR+A ++AK+  +        R  ++CSGCPHNTST VPEGS
Sbjct: 442  AARIARFH-TSDL---IKARLAFLDAKDAVLTKAVNTPPRPAYYCSGCPHNTSTKVPEGS 497

Query: 477  RALAGIGCHYM-TVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLL 535
             ALAGIGCH M T          + MGGEG  WIGQAPF+   HVFANLGDGTYFHSG L
Sbjct: 498  FALAGIGCHVMATAIYPEFNKLTTHMGGEGAPWIGQAPFSRIPHVFANLGDGTYFHSGYL 557

Query: 536  AIRASIAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEK 595
            AIRA++AA VN+TYKILYNDAVAMTGGQP+DG  SV  +A Q+AAEG  +I +V+++  +
Sbjct: 558  AIRAAVAAKVNMTYKILYNDAVAMTGGQPVDGTTSVPMIAQQMAAEGITRIALVSEDITR 617

Query: 596  YSAAIKLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKR 655
            YS    LP  V VH R ++D IQRELREV G +++IYDQTCA EKRRRRK+G YPDP +R
Sbjct: 618  YSDRSNLPALVTVHDRKDMDAIQRELREVSGVSVIIYDQTCAAEKRRRRKKGEYPDPDQR 677

Query: 656  AFINDAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEG 715
             FIN+AVCEGCGDC V+SNC S+ PLETE G KR I+QSSCNKD+SCV GFCPSFVT  G
Sbjct: 678  LFINEAVCEGCGDCGVQSNCTSILPLETEFGRKRAIDQSSCNKDYSCVKGFCPSFVTVTG 737

Query: 716  AQVKKPERHGV----SMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHL 771
             ++KK  + GV    S+D+  ALP+P +PG + P+ +L+ G+GGTGV+TIG L+GMAAHL
Sbjct: 738  GKLKK-SKTGVTSKDSVDDFGALPEPVIPGCDTPFNILINGIGGTGVITIGALMGMAAHL 796

Query: 772  ENKGVTVLDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVI 831
            E KG +VLDM G++QK G+V SHV+IA  P  + A RIA GEADL++GCD + +   D I
Sbjct: 797  EGKGASVLDMTGMSQKNGSVTSHVRIAQTPQAIRAQRIATGEADLILGCDMLTAGSHDAI 856

Query: 832  SKTQVGRTRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALI 891
            SK + GRTRA+VNT Q P  +F KNP W+FP       +  +VG++ DFI+AS LA AL+
Sbjct: 857  SKMRPGRTRAVVNTHQQPPGQFAKNPDWEFPFAEVRALIEESVGQSADFIDASRLATALM 916

Query: 892  GDAIFTNPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLS 951
            GD+I TN  +LGYAWQ+G LPL+  AL+RAIE+NG AVE NK +F WGR  A D    L+
Sbjct: 917  GDSIATNLFMLGYAWQRGELPLTEAALLRAIEMNGVAVESNKKSFLWGRRAAVD----LA 972

Query: 952  LTGKLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAES 1011
               ++   A+   V+++P +    L+KL+  R   LT YQD  YA  F   V +VR AE 
Sbjct: 973  RVERIAVPAQPV-VLRMPET----LDKLLTRRVAFLTGYQDERYAAGFAAVVQQVRQAE- 1026

Query: 1012 ALVGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNF 1071
            A++G G  L L  A ARNLSKLMAYKDEYEVARLYTD  F   L+ QFEG    DY+L+F
Sbjct: 1027 AVLGQGDKLSL--AVARNLSKLMAYKDEYEVARLYTDGSFTQHLQQQFEG----DYKLSF 1080

Query: 1072 WLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIG 1131
             LAPPL+AK+D +G L+K ++G   M +F VLAKL+ LRG   D+FG T ER+ ER L  
Sbjct: 1081 NLAPPLLAKKDAQGRLLKTQYGAWIMPVFRVLAKLRFLRGSKLDIFGYTEERQMERRLAL 1140

Query: 1132 EYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFR 1188
            EYR  +  L   L A N A AI +A LPD +RGFGHVKD  + +++T    LL +FR
Sbjct: 1141 EYRNTVLALLPQLRAGNLALAIEIAQLPDRVRGFGHVKDKAVLEMQTAQQDLLRRFR 1197


Lambda     K      H
   0.319    0.135    0.407 

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: 3200
Number of extensions: 127
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: 1197
Length of database: 1208
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1161
Effective search space:  1335150
Effective search space used:  1335150
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: 59 (27.3 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