GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Halomonas xinjiangensis TRM 0175

Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate WP_081948961.1 JH15_RS09265 hypothetical protein

Query= reanno::Marino:GFF2749
         (506 letters)



>NCBI__GCF_000759345.1:WP_081948961.1
          Length = 461

 Score =  301 bits (772), Expect = 3e-86
 Identities = 187/485 (38%), Positives = 262/485 (54%), Gaps = 39/485 (8%)

Query: 10  VAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKMQQQELD 69
           +AV+GAG MG GIAQ++AQ G    L+D + GAA A R+ +A+ L+RR+DKG+M   E  
Sbjct: 8   IAVIGAGIMGQGIAQISAQQGVITTLYDVQPGAAAAARERVAEALKRRIDKGRMSDAEAQ 67

Query: 70  DVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTSSISVTA 129
           + + R+      + + DA LV+EAI+EDL +KR L   LE +C A A+L +NTSS+S+ A
Sbjct: 68  ETLSRVRLAETFEALGDADLVVEAIVEDLAVKRDLFRRLEAICGAHALLCSNTSSLSIGA 127

Query: 130 LGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPVYATSTP 189
           +   ++ P+R+ G+HFFNPAP M LVEVV    TS+   D +   A   GK PV    +P
Sbjct: 128 IAEGLTAPQRVAGLHFFNPAPAMRLVEVVSAPDTSEATRDALLEFARTLGKTPVAVNDSP 187

Query: 190 GFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDVNYAVTS 249
           GFIVNR ARPFY E+L LL++   DA TLDA +   G F +G F L DL+G D+N   T+
Sbjct: 188 GFIVNRCARPFYGEALHLLEQGTADAETLDACLTCGGGFPLGPFALIDLVGVDINLKATT 247

Query: 250 SVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAHQSDESVI 309
           +++ ++ + PRF PS + +  V AG LG+KSGQGFY +    E P     P  Q D   +
Sbjct: 248 TLWEAFGRHPRFRPSPLIEAKVAAGELGKKSGQGFYRH--DRETPPSTALPPAQVDSLDV 305

Query: 310 IAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERAACEGVANLV 369
           +    P         L+  GL+        Q+  G    AL+       R   + V    
Sbjct: 306 LLAQLP---------LRLPGLS--------QVSDGHTAAALS-------RRHAQPV---T 338

Query: 370 LFDLAF-DYSKASRLALAPADQASDAA-----VSCACALLQKAGIEVSLIADRPGLVIMR 423
           LFD++   + K   + LA A      A     +  A  L    G+ +  + DRPGLV++R
Sbjct: 339 LFDVSLVPWPKERAMTLAFASHGLSEAEHVELIEAAATL----GVRLVEVPDRPGLVVLR 394

Query: 424 TVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQTSY 483
              ML  EA  A   GVAT   +D AM+ GLN+  GP    +RLG+  V   L    +  
Sbjct: 395 VATMLIGEARRALAEGVATADAMDTAMRLGLNFALGPWDMLERLGSEPVETTLAGAASED 454

Query: 484 AEDRY 488
              RY
Sbjct: 455 DRGRY 459


Lambda     K      H
   0.318    0.133    0.375 

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: 508
Number of extensions: 23
Number of successful extensions: 3
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: 506
Length of database: 461
Length adjustment: 34
Effective length of query: 472
Effective length of database: 427
Effective search space:   201544
Effective search space used:   201544
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 (21.7 bits)
S2: 52 (24.6 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