Alignments for a candidate for paaH in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Xanthobacter autotrophicus Py2

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_012116414.1 XAUT_RS22510 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000017645.1:WP_012116414.1
          Length = 789

 Score =  508 bits (1308), Expect = e-148
 Identities = 311/795 (39%), Positives = 446/795 (56%), Gaps = 33/795 (4%)

Query: 5   IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64
           I+K AV+G+GVMG+GIAAH+AN GI VLLLDIVP              + +  R+ ++ +
Sbjct: 18  IKKVAVIGAGVMGAGIAAHVANAGIEVLLLDIVP--------------EGAANRNAIAEK 63

Query: 65  AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVDE 124
           A++KLLK  PA   S +    +T GN+ED+   L   DWI+E V+E L++K+ ++A ++ 
Sbjct: 64  AVEKLLKADPAAFMSKRAAKLVTAGNIEDNLSDLASCDWIVEAVIERLDIKQALYAKIEA 123

Query: 125 HRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDIL 184
            R+ GS VSSNTS I + ++  G  + F+  FL THFFNP RY++LLEI+   ET+P  +
Sbjct: 124 ARRPGSAVSSNTSTIPLGDLTAGLPESFRRDFLITHFFNPPRYMRLLEIVAGPETNPATV 183

Query: 185 KFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLIG 244
             +  F +  LGK VVT KDTP FIANR+GTY L + V E  + G +V E D++ G   G
Sbjct: 184 AAVARFADVKLGKTVVTCKDTPGFIANRLGTYWLQLAVGEAFRLGLKVEEADAVMGRPFG 243

Query: 245 RPKSATFRTLDVVGLDTFAHVARNVYDKADGDE--KEVFRIPSFMNDMLEKGWIGSKAGQ 302
            PK+  F  +D+VGLD   HV  ++       +      R    ++ M+E G+IG K   
Sbjct: 244 FPKTGVFGLIDLVGLDLMPHVQGSLKRALPASDPFHATLRDEPLISKMIETGYIGRKGKG 303

Query: 303 GFYK----KEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGR 358
           GFY+      GK    +D  T  Y  + K   P LE      G    + AL+ +   AGR
Sbjct: 304 GFYRLNRENGGKAKEAIDLSTGAYRPQEKASVPELE-----DGGGKDIFALLSAPGTAGR 358

Query: 359 LLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQL 418
              ++ ++TL Y+A L+ E ADDI AID AM+ G+ W+ GPFE+ D IG  + A  L   
Sbjct: 359 YARSVMAKTLAYAARLVPEAADDIVAIDDAMRLGYNWKFGPFELIDKIGAARLAGLLAAD 418

Query: 419 GADMPGWIKEMLDKGNETFYIKENGTVFYYD-RGEYRAVKENKKRIHLQALKETKGVIAK 477
           G ++P  +    D     FY  ENG   Y    G YR V      + L  +K     + K
Sbjct: 419 GEEVPALLALAAD---TPFYRVENGKRQYLALDGSYRDVVRPDGVLLLADIKLKSQPLLK 475

Query: 478 NSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGA 537
           N  A+L D+GD V  LEF SKSN++   II M+ K L+  +  +K LVI N+G NF VGA
Sbjct: 476 NGSAALWDIGDGVVCLEFTSKSNSLDEGIITMLAKALKLVKDKHKALVIYNEGSNFSVGA 535

Query: 538 NLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARI 597
           NL + L       F EV+ ++   Q+T   +KY+  PVVAAP G+ LGGG E  L A+ +
Sbjct: 536 NLGLALFACNIGAFGEVEKLVATGQKTYQDMKYAPFPVVAAPSGLALGGGCEILLHASAV 595

Query: 598 QAASEAYMGLVESGVGLIPGGGG---NKELYINHLRRGHDPMNAAMKTFETIAMAKVSAS 654
           QA +E+Y+GLVE GVG++P  GG     E +    +    PM A  K FET++ A V+ S
Sbjct: 596 QAHAESYIGLVECGVGVLPAWGGCTAMLERWATDPKFPKGPMPAPSKVFETVSTATVAKS 655

Query: 655 AQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAALLL 714
           A EA+E+  L+E+D I++N+D LL DAK  A +L + G+ PP   +  +PG TG  A+ +
Sbjct: 656 AAEAKELKFLRESDGITMNRDRLLADAKAKALALVE-GYAPPKPVEFFLPGPTGKVAMDM 714

Query: 715 GAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAKSQ 774
                   G  ++HD  ++  LA V+ GG       V    +LE+ER+ F+ L     + 
Sbjct: 715 AVAGFAKRGMATKHDKVVSGVLAEVLTGGSADHIEPVPAARVLELERDGFMKLIRTTATL 774

Query: 775 ARMQHMLVKGKPLRN 789
            R++H+L  G+PLRN
Sbjct: 775 DRIEHILETGRPLRN 789


Lambda     K      H
   0.316    0.134    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: 1355
Number of extensions: 71
Number of successful extensions: 7
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: 789
Length of database: 789
Length adjustment: 41
Effective length of query: 748
Effective length of database: 748
Effective search space:   559504
Effective search space used:   559504
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: 55 (25.8 bits)

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

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Protein sequences (fasta format)
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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