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_012112645.1 XAUT_RS03135 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000017645.1:WP_012112645.1
          Length = 765

 Score =  437 bits (1123), Expect = e-126
 Identities = 283/795 (35%), Positives = 418/795 (52%), Gaps = 43/795 (5%)

Query: 5   IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64
           IRK  V+G+GVMGSGIAAHLAN G+ V+LLD+                +++   + +++Q
Sbjct: 4   IRKTGVIGAGVMGSGIAAHLANAGLDVVLLDV----------------EAATAAAAVTKQ 47

Query: 65  AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVDE 124
                   K      A     +  G++  D   L +AD IIE V E L+VK+ ++  ++ 
Sbjct: 48  L-------KAGGFMDAAFAERVVTGSVSSDMPMLSDADLIIEAVAERLDVKQGLYGRIEA 100

Query: 125 HRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDIL 184
            RK GSIVSSNTS I +  + EG  + F A FL THFFNP R + LLE++    T P+ L
Sbjct: 101 VRKPGSIVSSNTSTIPLSALVEGLPEGFAADFLVTHFFNPPRTMPLLELVAGPRTRPEAL 160

Query: 185 KFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLIG 244
           + +  FG+ VLGK VV  +DTP FIANR+G Y +   V E +  G  V   D+      G
Sbjct: 161 ETIRDFGDRVLGKSVVVCRDTPGFIANRVGNYWMAAAVNEAIALGLDVEVADAAISKPFG 220

Query: 245 RPKSATFRTLDVVGLDTFAHVARNVYDK-ADGDEKEVFRI-PSFMNDMLEKGWIGSKAGQ 302
            PK+  F  +D+VG+D  + V R+++D     D  + + + P+ +  M+ +  +G K+G 
Sbjct: 221 IPKTGIFGLMDLVGIDLMSMVLRSLHDALPPSDPMQDYPVEPALLARMVGEKRLGRKSGA 280

Query: 303 GFYK--KEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGRLL 360
           GF K   + K+    D VT  Y  + K++S AL+AA      K   +AL+  D  AGR  
Sbjct: 281 GFVKLSADRKSREVTDLVTGAYRPQKKVESDALDAA------KGDARALMQHDGAAGRYA 334

Query: 361 WNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQLGA 420
             +  + L Y+A +  EIAD   A+D AM+ G+GW  GPFE+ D +G      +LE+ G 
Sbjct: 335 SAVMEKALAYAARVTPEIADGPDAVDTAMRGGYGWAKGPFELIDQLGAGWLVARLEKRGV 394

Query: 421 DMPGWIKEMLDKGNETFYIKENGT-VFYYDRGEYRAVKENKKRIHLQALKETKGVIAKNS 479
            +P ++ +    G   FY  ENG        G  R V +    I L A++     +    
Sbjct: 395 PVPDFLAKAAAAGG--FYAIENGARTCLLPDGTRRKVAQADGVITLAAVQLASKPVEDWG 452

Query: 480 GASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGANL 539
            A L DLGD +A  E  SK N  G  ++  +   L   ++++KGLVIG+    F  GA++
Sbjct: 453 TARLWDLGDGIACFEIRSKMNTFGAPVLDALEATLARVQQSFKGLVIGSDAPLFSAGADI 512

Query: 540 AMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARIQA 599
            + L  V+          I R       +KY+  PVV A  G+  GGG E  L    IQA
Sbjct: 513 RVFLETVETSGPAAFGASIDRGHRLFKAVKYAPFPVVGAAAGLAFGGGCELLLHCRAIQA 572

Query: 600 ASEAYMGLVESGVGLIPGGGGNKELYINHLRRGH----DPMNAAMKTFETIAMAKVSASA 655
            +E  +GLVE  +G++PG GG KE+ +     GH     P+  A+  F  IA AKVS+SA
Sbjct: 573 HAELTIGLVEPRIGVVPGWGGCKEMLL-RFAEGHASAKGPVAPALAAFGVIAPAKVSSSA 631

Query: 656 QEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAALLLG 715
            EAR +  L+ TD I++N+D LL DAK  A +L +  + PP    + + G +G +AL   
Sbjct: 632 FEARRLGFLRPTDGITMNRDRLLADAKAKALALAE-DYAPPAPPSLTLSGPSGASALRNV 690

Query: 716 AEQMKLSGYISEHDFKIAKKLAYVIAGG-KVPFGTEVDEEYLLEIEREAFLSLSGEAKSQ 774
            +   ++G ++ HD  + + LA V+ GG        VDE+ +  +ER AF++L GE  + 
Sbjct: 691 LDTEAMAGRLTAHDLVVGEALASVLTGGPDADPARPVDEDAVTALERAAFIALLGEPATL 750

Query: 775 ARMQHMLVKGKPLRN 789
            R++HML  GKPLRN
Sbjct: 751 ERIRHMLATGKPLRN 765


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: 1246
Number of extensions: 52
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: 765
Length adjustment: 41
Effective length of query: 748
Effective length of database: 724
Effective search space:   541552
Effective search space used:   541552
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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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