Alignments for a candidate for ofo in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Sulfuritalea hydrogenivorans DSM 22779

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_041097026.1 SUTH_RS03175 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000828635.1:WP_041097026.1
          Length = 1155

 Score = 1379 bits (3569), Expect = 0.0
 Identities = 702/1163 (60%), Positives = 851/1163 (73%), Gaps = 35/1163 (3%)

Query: 17   LANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQ 76
            L  ++LEDKY L  GRV+++GTQALVRL +LQR+RD  AGLNTAG++SGYRGSPLG LDQ
Sbjct: 5    LRTITLEDKYALASGRVFLTGTQALVRLLLLQRQRDALAGLNTAGYVSGYRGSPLGGLDQ 64

Query: 77   SLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRT 136
            +LWKA+ HLA   +VFQ G+NEDLAAT++WG+QQVN+ P A+ +GVFGMWYGKGPGVDR 
Sbjct: 65   ALWKARPHLAQSHVVFQPGVNEDLAATALWGTQQVNLSPGAKHDGVFGMWYGKGPGVDRC 124

Query: 137  SDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDY 196
             DVFKHANSAG+ +HGG+L +AGDDHAA+SST+AHQSEH FKA  +PVL P+ VQ+YLD 
Sbjct: 125  GDVFKHANSAGTWKHGGILAVAGDDHAARSSTVAHQSEHAFKAAMMPVLVPAGVQDYLDL 184

Query: 197  GLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPP 256
            GLH WAMSRYSG WV  K V D VESSASV++ P RV IVLP D+ LP GGLNIRWPD  
Sbjct: 185  GLHGWAMSRYSGCWVGFKAVADTVESSASVDISPDRVRIVLPDDYALPAGGLNIRWPDDR 244

Query: 257  LEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDE 316
            L QEARLLD+K YA LAY RANK++++ ID+P+ R GI+T GK+YLD RQA  +LG+DD 
Sbjct: 245  LLQEARLLDHKLYAALAYCRANKLNQVVIDAPNPRLGIITTGKSYLDVRQAFDDLGIDDA 304

Query: 317  TCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRP 376
              A IGIRLYKVG VWPLE+ G R FAEGL+EILVVEEKRQ++EY LKEELYNWR+DVRP
Sbjct: 305  LAAEIGIRLYKVGMVWPLESDGVRRFAEGLEEILVVEEKRQLIEYQLKEELYNWREDVRP 364

Query: 377  KVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDK-FELPADVRARIAA 435
            +V GKFDEK    GEW++P   WLLPA  ELSPA IAR IA R+ + F  P     RI  
Sbjct: 365  RVIGKFDEK----GEWALPNGRWLLPASGELSPAQIARVIADRIGRHFTSP-----RIRE 415

Query: 436  RIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRST 495
            R+A+IEAKE++ A P +   R P+FC GCPHNTST VPEGSRALAGIGCH+M +WM+RST
Sbjct: 416  RLAIIEAKERS-AAPAIQVARTPYFCPGCPHNTSTCVPEGSRALAGIGCHFMVLWMNRST 474

Query: 496  STFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYND 555
            +T+S MGGEG AW+GQAPF   +HVF NLGDGTYFHSG LAIRA++A+GVN TYKILYND
Sbjct: 475  ATYSHMGGEGAAWMGQAPFTEQRHVFVNLGDGTYFHSGSLAIRAAVASGVNATYKILYND 534

Query: 556  AVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELD 615
            AVAMTGGQP+DG L+V  +A+Q+ AEG   +VVVTD   +      LP GV + HRDELD
Sbjct: 535  AVAMTGGQPVDGNLTVPQIAHQLHAEGVHHVVVVTDGTARAYGHPDLPHGVPIRHRDELD 594

Query: 616  RIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNC 675
             IQRE+RE PG + +IYDQTCA EKRRRRKRG   DP +R FIN+AVCEGCGDC V+SNC
Sbjct: 595  AIQREMRECPGVSAIIYDQTCAAEKRRRRKRGKMIDPPRRLFINEAVCEGCGDCGVQSNC 654

Query: 676  LSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSM---DNLP 732
            L+V P+ETE G KR I+QS+CNKD+SC  GFCPSFV+  G  VKK      S    D + 
Sbjct: 655  LAVVPVETEFGRKRAIDQSACNKDYSCEKGFCPSFVSVLGGGVKKGRGLAGSTNGGDFIA 714

Query: 733  ALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVL 792
              P P L     PYG+L+TGVGGTGVVTIG L+GMAAH++ KGVTVLDM GLAQKGGAV 
Sbjct: 715  VPPAPTLASTADPYGILITGVGGTGVVTIGALIGMAAHIDGKGVTVLDMTGLAQKGGAVF 774

Query: 793  SHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAE 852
            SHV+I   P+ +HA R+A GEAD VIG D IV+A  D +++ Q GRTR +VN A+TPTA+
Sbjct: 775  SHVRICDDPEAIHAVRVATGEADAVIGGDVIVTASPDALTRMQSGRTRVVVNCAETPTAD 834

Query: 853  FIKNPKWQFPGLSAEQDVRNAVGE-ACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWL 911
            F +NP WQFP    +  V   VG  A  F++AS LAV L+GD+I +N  +LGYAWQ+G +
Sbjct: 835  FTRNPDWQFPLARMQAVVGETVGAGAAHFVDASDLAVRLLGDSIASNLFLLGYAWQQGLV 894

Query: 912  PLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTS 971
            P+S DA+ RAIELNGTAV  ++AAF WGR  AHDP  V +               K+   
Sbjct: 895  PVSWDAIDRAIELNGTAVPLSRAAFLWGRRAAHDPAGVAAYARP-----------KIAVP 943

Query: 972  SGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLS 1031
                L++LIA R   LT YQDAAYA+ +R  V ++R AE+ +  +     LTE  A NL 
Sbjct: 944  PAPTLDELIAKRVRFLTEYQDAAYAERYRTQVEKIRTAEAFIDSS----QLTETVAHNLF 999

Query: 1032 KLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEK-GHLVKR 1090
            KLMA KDEYEVARLY +  FL K+  +FEG    DY L F LAPPL+A+ D K G + K 
Sbjct: 1000 KLMAIKDEYEVARLYAETDFLQKIGERFEG----DYTLQFHLAPPLLARPDPKTGKVKKL 1055

Query: 1091 RFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHA 1150
             FGP  +  F  LAK +  RG  +DVFG++AER+ ER+L+ +Y A L  +   L      
Sbjct: 1056 AFGPWMLTGFKWLAKARRYRGSRWDVFGRSAERQLERSLLADYEADLARMAGKLDRTTLG 1115

Query: 1151 TAITLASLPDDIRGFGHVKDDNL 1173
             AI LA+LP+ IRGFGHVK  N+
Sbjct: 1116 DAIALANLPEKIRGFGHVKRRNI 1138


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: 3503
Number of extensions: 160
Number of successful extensions: 10
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: 1155
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1108
Effective search space:  1274200
Effective search space used:  1274200
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 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