GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Novosphingobium barchaimii LL02

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_059153517.1 V474_RS22775 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_001046635.1:WP_059153517.1
          Length = 774

 Score =  513 bits (1322), Expect = e-149
 Identities = 306/798 (38%), Positives = 445/798 (55%), Gaps = 33/798 (4%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M   IRK  V+G+G MG+GIAA +AN G+PVLLLDIVP D                 R+ 
Sbjct: 1   MSDTIRKVCVIGAGTMGAGIAAQVANAGVPVLLLDIVPKDAGN--------------RNA 46

Query: 61  LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120
           ++  A+ K+LK +PAP  S      +  GN+ED  EK+ E DW+IE V+E L++K+ ++A
Sbjct: 47  IAEGAVAKMLKTEPAPFMSKSAAKLVETGNIEDHLEKIAECDWVIEAVIERLDIKQGLYA 106

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            ++  ++ G+ VSSNTS I + ++ EGRS  F+  FL THFFNP RY++LLEI+    TD
Sbjct: 107 RIEAVKRDGTAVSSNTSTIPLAQLVEGRSAAFQRDFLITHFFNPPRYMRLLEIVTGPATD 166

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240
             I   +  F +  LGK VV A DTP FIANRIGTY + + +      G  V   D+I G
Sbjct: 167 TAIAAKVERFSDAALGKTVVRANDTPGFIANRIGTYWIQLGLNAAFDMGLTVELADAIAG 226

Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE--KEVFRIPSFMNDMLEKGWIGS 298
             +G PK+  F  +D+VG+D   H+  ++      D+    + R    +  M+ +G+ G 
Sbjct: 227 KPMGVPKTGIFGLVDLVGIDLMPHLQASLTSTLPKDDPYHAIARTMPLIEKMIGEGYTGR 286

Query: 299 KAGQGFY---KKEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDR 355
           K   GFY   K+ G+    +D  +  Y E  +   P+  A       K  ++AL+ +  +
Sbjct: 287 KGKGGFYRLNKEMGRRKETIDLASGEYRETIRAFGPSGAAG------KGDLRALVETKGK 340

Query: 356 AGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKL 415
            G   W +   TL Y+A L+   A D+ AID AMK G+ W+ GPFEM D +G    A++L
Sbjct: 341 IGDYAWAVLGGTLAYAAALVPSAAGDVVAIDDAMKLGYNWKAGPFEMIDKLGAAWLAQRL 400

Query: 416 EQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD-RGEYRAVKENKKRIHLQALKETKGV 474
           E  G  +P  +K     G+ TFY  E+G   Y D  G YR +K  +  + L  +K     
Sbjct: 401 ESEGKPVPEILK---IAGDRTFYRVEDGKRQYLDLDGTYRDIKRPEGVLKLSDIKLASKP 457

Query: 475 IAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFC 534
           + +N  A+L D+GD V  LEF  K NA+  D++++I + +   +  YK LV+ N   +F 
Sbjct: 458 LLRNGSAALWDVGDGVVALEFTGKMNALDGDVMKLIVEAIPLVKAKYKALVVYNDADSFS 517

Query: 535 VGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPA 594
            GANL + L  V    + E++ +I   Q     +KY+  PVV AP G+ +GGG E  L  
Sbjct: 518 AGANLGLALFAVNIAAWGEIEKLIAGGQMAYKGLKYAPFPVVGAPAGLAVGGGCEILLHC 577

Query: 595 ARIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMAKV 651
             +QA +E YMGLVE GVGLIPG GGN E+   +  +      PM A  K FET++ A V
Sbjct: 578 DAVQAHAELYMGLVECGVGLIPGWGGNGEMLDRWQKNKGMPKGPMPAVAKVFETVSTASV 637

Query: 652 SASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAA 711
           S SA +A+E+  L+  D +++N+D LLYDAKQ A SL + G+  P     ++PGE+G  A
Sbjct: 638 SRSAAQAKELLFLRADDGVTMNRDRLLYDAKQKALSLVE-GYAAPEAPTFRLPGESGRTA 696

Query: 712 LLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEA 771
           L + AE     G  +++D  ++  LA V++GG+      V E  LL++ERE F+ L  E 
Sbjct: 697 LGMAAEGFHKQGKATDYDMVVSAALAGVLSGGEADLVDTVSEAELLKLERETFMRLVREP 756

Query: 772 KSQARMQHMLVKGKPLRN 789
           +S  R++HML  GKPLRN
Sbjct: 757 RSIVRVEHMLETGKPLRN 774


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: 1434
Number of extensions: 71
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: 774
Length adjustment: 41
Effective length of query: 748
Effective length of database: 733
Effective search space:   548284
Effective search space used:   548284
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.

Links

Downloads

Related tools

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