Alignments for a candidate for paaH in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Desulfitobacterium hafniense DCB-2

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_015945288.1 DHAF_RS22630 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000021925.1:WP_015945288.1
          Length = 795

 Score =  780 bits (2014), Expect = 0.0
 Identities = 410/795 (51%), Positives = 534/795 (67%), Gaps = 12/795 (1%)

Query: 5   IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64
           I K AVLGSGVMGS IAAHLAN GIP +LLDIVP  L  EEE  GLT  S +VR+R +  
Sbjct: 3   IYKVAVLGSGVMGSTIAAHLANAGIPSILLDIVPPSLLPEEEAAGLTLASPQVRNRFAAS 62

Query: 65  AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVDE 124
              KL+K  PAPL   +    I  GN EDD  +L+E DW+IEVVVE L++K  +F  V +
Sbjct: 63  NKAKLIKMNPAPLFVPEFADRIEVGNFEDDLPRLQEVDWVIEVVVERLDIKIDLFKKVAQ 122

Query: 125 HRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDIL 184
           H + G+IV+SNTSGIS++ M EG  ++F   F GTHFFNP RY+KL E+IP   TDP ++
Sbjct: 123 HVRPGTIVTSNTSGISLKSMTEGLPEEFTKSFFGTHFFNPPRYMKLFELIPGPNTDPTVI 182

Query: 185 KFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLIG 244
           + M  F E VLGKGVV AKDTPNFIANRIG +GL  T++EM + G  + EVD++TGP++G
Sbjct: 183 QEMEEFAERVLGKGVVYAKDTPNFIANRIGVFGLAATIREMQRSGLTIDEVDALTGPVMG 242

Query: 245 RPKSATFRTLDVVGLDTFAHVARNVYDKADGDEKEVFRIPSFMNDMLEKGWIGSKAGQGF 304
           RPKSA+FRT+D+VGLDTF HVA NV D    +EKE F +P F++ M++ GW+G K+ QGF
Sbjct: 243 RPKSASFRTVDMVGLDTFVHVANNVGDNVP-EEKEFFVMPDFIHTMIKNGWLGDKSKQGF 301

Query: 305 YKK----EGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGRLL 360
           YKK    EGK +  LDP T+ Y  + K+K   L+ AK A G K KMK L+   D      
Sbjct: 302 YKKVKTAEGKEVLVLDPHTMEYVPKKKVKFACLDKAKNAGGLKDKMKTLVNGKDPGAEFA 361

Query: 361 WNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQLGA 420
           WN+  + LLY+A L  +IADD+ A+D  MK GF WE+GPFE WDA+G+K +AE++   G 
Sbjct: 362 WNVLKEVLLYAARLAPQIADDLTALDAGMKLGFNWEMGPFETWDALGVKATAERIAAEGG 421

Query: 421 DMPGWIKEMLDKGNETFYIK-ENGTVFYYDRGEYRAVKENKKRIHLQALKETKGVIAKNS 479
            +P  + ++L +G ++FY K E G   YY  GEY+    +     L+   +    I  NS
Sbjct: 422 TLPEIVAKLLAEGKDSFYEKTEGGDTLYYAGGEYKEKAASPYSFSLKKAHKQGKKIFGNS 481

Query: 480 GASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGANL 539
           GASL+D+GD VA LEFHS +N+IG DI+ MIHK L E E+NY G+VIG+QGKNF VGANL
Sbjct: 482 GASLVDMGDGVACLEFHSPNNSIGGDIMNMIHKSLAEVEKNYLGMVIGSQGKNFAVGANL 541

Query: 540 AMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARIQA 599
            +I+ME ++ N+ ++D ++R FQ   M +KY+ KPVVAAP+GMTLGGGTE CL +  IQ 
Sbjct: 542 MLIMMEAEEGNWDDLDLMVREFQRGTMALKYAKKPVVAAPYGMTLGGGTEVCLHSHAIQP 601

Query: 600 ASEAYMGLVESGVGLIPGGGGNKELYINHLRRGHDPMNAA-----MKTFETIAMAKVSAS 654
           A+E YMGLVE GVGLIPGGGG KE+ +  +      +  A      K FE +AMA+VS S
Sbjct: 602 AAETYMGLVELGVGLIPGGGGTKEMALRAMEGILPGVVVAPDYFFAKRFEVVAMAQVSTS 661

Query: 655 AQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAALLL 714
           A+ AR++  L+ +D+ S+N DH+L DAK     L    +RP + +KVK  G    A L +
Sbjct: 662 AEMARKLGFLRASDRCSMNADHVLLDAKARVLDL-ARDFRPIIPQKVKAAGPGVCAFLEM 720

Query: 715 GAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAKSQ 774
               MK   YISE+D  + KKLAY + GG V  GT VDE+YLL++ERE FLSL+GE K+ 
Sbjct: 721 ALYGMKEGRYISEYDAHLGKKLAYAMTGGDVLAGTLVDEQYLLDLEREVFLSLAGEPKTL 780

Query: 775 ARMQHMLVKGKPLRN 789
            R++HML K KPLRN
Sbjct: 781 DRIRHMLTKNKPLRN 795


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: 1549
Number of extensions: 64
Number of successful extensions: 6
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: 795
Length adjustment: 41
Effective length of query: 748
Effective length of database: 754
Effective search space:   563992
Effective search space used:   563992
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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