Alignments for a candidate for ofo in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Marinobacter adhaerens HP15

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate GFF880 HP15_859 pyruvate ferredoxin/flavodoxin oxidoreductase

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



>FitnessBrowser__Marino:GFF880
          Length = 1172

 Score = 1124 bits (2907), Expect = 0.0
 Identities = 590/1175 (50%), Positives = 793/1175 (67%), Gaps = 38/1175 (3%)

Query: 17   LANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQ 76
            L +  LED+Y  E GRV+++GTQALVR+P++Q   DR  GLNTAG +SGYRGSPLGA+DQ
Sbjct: 8    LDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQ 67

Query: 77   SLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRT 136
            +LW+AK  L  + I F   +NEDLAAT + G+QQV    D + EGVFG+WYGKGPGVDR 
Sbjct: 68   ALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRA 127

Query: 137  SDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDY 196
             D  KH  + GSS HGGVLV+AGDDH   SS++ HQS+  F +  +P + P+N+ EYL++
Sbjct: 128  GDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEF 187

Query: 197  GLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPP 256
            GL  +A+SRYSG WV  K +++ VES+ASVE+ P   + V P DF  P  GL+ RWPD P
Sbjct: 188  GLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLHYRWPDLP 246

Query: 257  LEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDE 316
              Q    +++K  A  A+ RAN+IDR   D+  ARFGI+T GK +LD  +AL  LG+D++
Sbjct: 247  GPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDED 306

Query: 317  TCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRP 376
                +G+ +YKVG VWPLE  G   F  G +E+LV+EEKR I+E  +KE +         
Sbjct: 307  KARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEV 366

Query: 377  KVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIAAR 436
             + GK DE               L+P   ELSP ++A  +A RL +F    D   R+A  
Sbjct: 367  LITGKQDELGRP-----------LIPYVGELSPKLVAGFLAARLGRF-FEVDFSERMAEI 414

Query: 437  IAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTS 496
             A+  A++          +R P+FCSGCPHNTST VPEGS+ALAGIGCH+M  WM R+T 
Sbjct: 415  SAMTTAQDPG------GVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTE 468

Query: 497  TFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDA 556
            +  QMGGEGV WIG++ + G+ HVF NLG+GTYFHSG +AIR ++AAG+NITYKIL+NDA
Sbjct: 469  SLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDA 528

Query: 557  VAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKL-PQGVEVHHRDELD 615
            VAMTGGQP+DG+++V  +A Q+AAEG  ++VV++DEPEKY     L P+ V  H R ELD
Sbjct: 529  VAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELD 588

Query: 616  RIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNC 675
            ++QRELR++PG T+LIYDQTCA EKRRRRKR  +PDPAKRAFIN  VCEGCGDCSV+SNC
Sbjct: 589  QVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNC 648

Query: 676  LSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKP---ERHGVSMDNLP 732
            LSV P +TELG KR+I+QSSCNKDFSCVNGFCPSFVT EG Q++K    +   V    L 
Sbjct: 649  LSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLA 708

Query: 733  ALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVL 792
             +P P LP +   Y +LV GVGGTGVVT+G L+ MAAHLE++G +VLD  G AQKGG VL
Sbjct: 709  DIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVL 768

Query: 793  SHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAE 852
            S+V++A  PD+LH  RI+ G+AD VI CD +V++    +S  +   TR + N A+ PTA+
Sbjct: 769  SYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTAD 828

Query: 853  FIKNPKWQFPGLSAEQDVRNAVGE-ACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWL 911
            ++               ++NAVGE   D ++A+G+A  L+GD +F+N ++LG+AWQKG L
Sbjct: 829  YVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLL 888

Query: 912  PLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTS 971
            PLS  AL++AIELNG A+++NK AF WGR  A DP  V  L     + A+  EV   PT 
Sbjct: 889  PLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDD--SNAQVVEVKPEPT- 945

Query: 972  SGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLS 1031
                L++LI  R +HL  YQ+  +A  +RD V+ VR AE +L      L LT A A+ L 
Sbjct: 946  ----LDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESL--GETNLLLTRAVAQQLY 999

Query: 1032 KLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMA-KRDEKGHLVKR 1090
            + MAYKDEYEVARL+ +  F+ ++   FEG    D++++F LAPPL++ + D +G   KR
Sbjct: 1000 RFMAYKDEYEVARLFAETDFMKEVNETFEG----DFKVHFHLAPPLLSGETDAQGRPKKR 1055

Query: 1091 RFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHA 1150
            RFGP   + F +LAKL+GLRG   D F  +A+R+ +RA++ +Y++L++ + R L+A+N+ 
Sbjct: 1056 RFGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYE 1115

Query: 1151 TAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLE 1185
            T + LA LP D+RG+G V++     +R + T L++
Sbjct: 1116 TFLQLAELPADVRGYGPVREQAAESIREKQTQLIK 1150


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: 3063
Number of extensions: 121
Number of successful extensions: 12
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: 1172
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1125
Effective search space:  1293750
Effective search space used:  1293750
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 Sep 17 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, or view the source code.

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