GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofoA in Marinicella litoralis KMM 3900

Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_099019123.1 CCS90_RS08560 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::P72578
         (632 letters)



>NCBI__GCF_002591915.1:WP_099019123.1
          Length = 609

 Score =  166 bits (421), Expect = 2e-45
 Identities = 168/627 (26%), Positives = 272/627 (43%), Gaps = 88/627 (14%)

Query: 12  GTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRSNTQKIDILVS 71
           G+G  +A N+F  AV   G  +     + SNI+G  ++F + I++          D +V+
Sbjct: 19  GSGSASANNLFSKAVFRLGVPVSSKNVFPSNIQGLPTWFEVRINEHGYLGRRGGYDFIVA 78

Query: 72  FDAETVFQHFYDVKD--ILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQGYETTVKGA 129
            + +T+++ + ++       Y+ +                 +R+ D   +Q         
Sbjct: 79  DNGQTMYKDYQELLPGGYFFYDSS-----------------KRLPDSFNRQ--------- 112

Query: 130 LEYASKNNVTLIPVNYDEIAKKVADEMKVPLSVTERVKNIVGITISYKLLGLDVNYLIEA 189
                  +V  I +   EI      + +      +  KNI+ +     L  +D +   ++
Sbjct: 113 -------DVVPIGIPLTEICNANYTDPRQ----RQIFKNIIYVGALAYLFEMDFSVFEQS 161

Query: 190 INSTF-KQDLYRKMNELAVKDSYDIVESRYNLKPSSKERRR------FWLDGNTAVAIGK 242
           I S F K+    + N  A+   +   E  +N        RR        ++GN A  +G 
Sbjct: 162 IKSLFAKKAKLIEPNIKALMLGFSYAEEHHNAVCELNIHRRDLNGEQILMEGNAAAGLGA 221

Query: 243 IYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQAEDELAAINMAI 302
           ++ G     +YPITP++      E +      D  TG  K     +VQAEDELAAI + I
Sbjct: 222 VFAGATVAGWYPITPSTSVIEAFEKYCKAYRVDQHTGKNK---FAIVQAEDELAAIGIVI 278

Query: 303 GAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGLPTRTAQSDLIF 362
           GA+  G RA TATSGPG SLM E LG A  +E+PV++    R GPSTG+PTRT QSDLI 
Sbjct: 279 GASWNGARAFTATSGPGISLMSEFLGLAYFSEIPVMLMDIQRTGPSTGMPTRTQQSDLIA 338

Query: 363 PIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLA-NSYSTIPYEE 421
             +A HG+   ++L   +  E F   +   +LAE+ QTPVI + +  L  N +   P E 
Sbjct: 339 AAYASHGDTKNVLLFPANPKECFDMTVKGFDLAERLQTPVILMSDLDLGMNVHQCDPIE- 397

Query: 422 LELDKLKAERGKIVESGDISYKRFKFTE------DGISPRAFLG----KATMYYTGDEHN 471
              D+   +RGK++    ++    K+        DGI  R   G    K   +  G  H+
Sbjct: 398 -WDDQQVYDRGKVLNEKQLNELPEKWGRYLDVDGDGIPYRTIPGTHPEKGAYFTRGSSHD 456

Query: 472 EEGHISEDVVNRTMMYEKRMKKLEVADKEIPE--------ESRVKIYG--DLNSRNLIIT 521
           E    +ED        ++ + K + A K +P         +  V  YG  D +S+  +  
Sbjct: 457 EYAAYTEDGEVYARGMQRLLLKWDTAKKTVPAAEISGYTCQVGVIFYGTSDYSSKEAL-- 514

Query: 522 WGSPTGVLRDILEESNFDFTLLQIRMFSPFPKNLVSKLMEGRDKIITVEGNYLAQ--TSL 579
                 +LRD   +   D   ++I+ F PF +  V+  +E  D I  +E N  AQ  T L
Sbjct: 515 -----AILRD---KQTID--SMRIKAF-PFGEE-VNTFVEKHDVIFVIEQNRDAQMKTLL 562

Query: 580 LVKMYTGKDVTNSILKWNGRPFLRDEL 606
           + ++         +L  +G P   + L
Sbjct: 563 VNELAINPQKMIEVLNIDGMPITAEYL 589


Lambda     K      H
   0.316    0.135    0.382 

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: 860
Number of extensions: 52
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 632
Length of database: 609
Length adjustment: 37
Effective length of query: 595
Effective length of database: 572
Effective search space:   340340
Effective search space used:   340340
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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