Alignments for a candidate for paaH in Erythrobacter marinus HWDM-33

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Erythrobacter marinus HWDM-33

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_047093433.1 AAV99_RS07705 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_001013305.1:WP_047093433.1
          Length = 776

 Score =  540 bits (1390), Expect = e-157
 Identities = 306/795 (38%), Positives = 464/795 (58%), Gaps = 34/795 (4%)

Query: 5   IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64
           I+K  V+G+G MG+GIAA +AN GIPVLLLDI+P +               + R+ ++  
Sbjct: 6   IKKVCVIGAGTMGAGIAAQVANAGIPVLLLDILPKE--------------GDNRNAVAEG 51

Query: 65  AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVDE 124
           A+ K+LK +PAP    +    +  GN+ED   K+ E DW++E ++E L++K+ ++A ++ 
Sbjct: 52  AVAKMLKTEPAPFMGKRAAKLVETGNIEDHLGKVAECDWVVEAIIERLDIKQDLYAKLEA 111

Query: 125 HRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDIL 184
            R  G+ VSSNTS I + ++ +GRSD FK  FL THFFNP RY++L+EI+    ++ + +
Sbjct: 112 VRTPGTAVSSNTSTIPLAQLTDGRSDAFKQDFLITHFFNPPRYMRLIEIVAGPHSNAETV 171

Query: 185 KFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLIG 244
             ++ F +  LGK VV A+D+P FIANR+GT+ +  +V      G  V E D I G  +G
Sbjct: 172 ARVSDFVDRKLGKSVVDAEDSPGFIANRVGTFWIQASVNAAFDLGVTVEEADEIGGRPMG 231

Query: 245 RPKSATFRTLDVVGLDTFAHVARNVYDKADGDEK--EVFRIPSFMNDMLEKGWIGSKAGQ 302
            PK+  F  +D++G+D   H+ +++      D+   ++ R    + DM+E G+ G K   
Sbjct: 232 VPKTGIFGLIDLIGIDLMPHLMKSLTSTLPADDPYVKIARSEKLIEDMIETGYTGRKGLG 291

Query: 303 GFYKKE----GKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGR 358
           GFY+      GK +   D   L  GE      P L     AKG    + ALI +  + G 
Sbjct: 292 GFYRINREGGGKVMESKD---LKSGEYRAAARPGLVRGPAAKG---DLGALIEAPGKVGA 345

Query: 359 LLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQL 418
             W +   TL Y+A ++ E    +  +D AMK G+ W++GPFEM D IG  +  EKLE  
Sbjct: 346 YAWAVLGPTLAYAASIVPEATKSVVGVDDAMKLGYNWKMGPFEMIDRIGAAKLREKLEAS 405

Query: 419 GADMPGWIKEMLDKGNETFYIKENGTVFYYDR-GEYRAVKENKKRIHLQALKETKGVIAK 477
              +P  ++++   G++TFY  ENG   Y+   G Y  V+  +  + L+ +K     + K
Sbjct: 406 DIPVPAILQQV---GDQTFYRIENGKRQYFGTDGAYHDVERAEGVLLLEDIKLASEPLMK 462

Query: 478 NSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGA 537
           NS A+L D+GD V  LEF  K NA+  +++++I K +   + +YK LV+ N+G NF  GA
Sbjct: 463 NSSAALWDVGDGVVALEFTGKMNALDGEVMKLIQKAIPLVKSDYKALVVYNEGSNFSAGA 522

Query: 538 NLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARI 597
           NL + L  +    + EV+  IR  Q+    +KY+  PVV+APFG+ LGGG E  L +  I
Sbjct: 523 NLGLALFALNIAAWSEVEKSIRGGQDAYKALKYAPFPVVSAPFGLALGGGCEILLNSDAI 582

Query: 598 QAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMAKVSAS 654
           QA +E Y GLVE+GVG+IPG GG  E+   + ++ R+   PM A  K FE ++ A V+ S
Sbjct: 583 QAHAETYTGLVETGVGIIPGWGGCGEMLSRWADNPRQPKGPMPAVSKVFEIVSTATVAKS 642

Query: 655 AQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAALLL 714
           A EA+++  L+ TDQI++N+D LL+DAKQ A ++ D G+  P K + ++PG TG AAL L
Sbjct: 643 AAEAKDVGFLRHTDQITMNRDRLLHDAKQRALAMVD-GYEAPEKPEYRLPGPTGKAALDL 701

Query: 715 GAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAKSQ 774
             +     G  ++HD  +A +LAYV++GG       V E  +L++E EAF+ L+   KSQ
Sbjct: 702 AVDSFHKQGKATDHDVTVAGELAYVLSGGDTDMIDTVTEAQMLKLEVEAFMRLARNPKSQ 761

Query: 775 ARMQHMLVKGKPLRN 789
           AR++HML  GKPLRN
Sbjct: 762 ARVEHMLETGKPLRN 776


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: 1393
Number of extensions: 79
Number of successful extensions: 8
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: 776
Length adjustment: 41
Effective length of query: 748
Effective length of database: 735
Effective search space:   549780
Effective search space used:   549780
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 2024 update 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