Alignments for a candidate for fadB in Geotalea uraniireducens Rf4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Geotalea uraniireducens Rf4

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_011938497.1 GURA_RS08095 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000016745.1:WP_011938497.1
          Length = 795

 Score =  677 bits (1746), Expect = 0.0
 Identities = 375/802 (46%), Positives = 507/802 (63%), Gaps = 23/802 (2%)

Query: 3   KHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLS 62
           K I KAAVLGSGVMG+ IAAHLAN GI VLLLDIVP + +  E   GLT     VR+R++
Sbjct: 2   KQINKAAVLGSGVMGATIAAHLANAGIQVLLLDIVPREPSDAETAAGLTLADRAVRNRIA 61

Query: 63  RQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA-L 121
           +  +  LLK KPAP       SYI  GN EDD  +LKE DW+IEVV+EN+E+KKK+F+  
Sbjct: 62  QAGLDGLLKMKPAPFFIPGYASYIEVGNFEDDMARLKECDWVIEVVIENMEIKKKLFSEK 121

Query: 122 VDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDP 181
           V  + K G+++S+NTSG+SV EMAE   D+ + +FL THFFNP RY++LLEI+  + TDP
Sbjct: 122 VAPNMKDGAVLSTNTSGLSVNEMAESLPDNIRKNFLVTHFFNPPRYMRLLEIVSCRYTDP 181

Query: 182 DILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGP 241
            + + M AF    LGKG+V AKDTPNFIANRIG Y +   V+ M+     V EVD I GP
Sbjct: 182 AVAEKMAAFIGKRLGKGIVYAKDTPNFIANRIGVYAICNCVRNMMAMEMTVEEVDKIAGP 241

Query: 242 LIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSKA 300
              RPKSA FRT D+VG+DT  HVA N Y+    DE +E+FR P F+ +M+ KG +G+K+
Sbjct: 242 ATARPKSAAFRTADLVGIDTLQHVANNSYELLVNDEERELFRFPDFIREMVGKGLLGNKS 301

Query: 301 GQGFYKK----EGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRA 356
            QGF+KK    +  TI+  D  +  Y E    K  ++EAAK       +++A+I   D+A
Sbjct: 302 KQGFFKKAKGEKCSTIFFYDYKSGEYVEAQNPKFASVEAAKSIDDPAKRLQAVITGTDKA 361

Query: 357 GRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLE 416
            +  W     TL+Y+   + EIADDI  ID AMKWGF WELGPFEM DAIG+    E+ E
Sbjct: 362 AQFAWKNMRDTLIYTFNRIPEIADDIVNIDNAMKWGFNWELGPFEMLDAIGVGYFVERAE 421

Query: 417 QLGADMPGWIKEMLDKGNETFYIKENGTVFYYDRGE--YRAVKENKKRIHLQALKETKGV 474
           + GA +P  +K +     E FY   +G  +YY   +  YR +      ++L  LK + G+
Sbjct: 422 KDGAPVPAGLKAV-----EQFYKFADGKNYYYSLADKSYREIARKAGHVNLSVLKRSGGM 476

Query: 475 IAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFC 534
           + KNSGAS++DLGD V  LEFH+K NAIG +I+ M+HKG++ +E    GLVI N+G  F 
Sbjct: 477 VEKNSGASVVDLGDGVFCLEFHTKMNAIGNEILSMVHKGIKRSEEEGVGLVIANEGGLFS 536

Query: 535 VGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPA 594
            GANL +++M + +  + E+   ++ FQ+ MM IKYS  PVVAAP  +T+GGG E CL A
Sbjct: 537 AGANLMLLVMGIAEGAYDEIAMTVKNFQKAMMAIKYSKIPVVAAPHNLTMGGGCETCLHA 596

Query: 595 ARIQAASEAYMGLVESGVGLIPGGGGNKELYINHLRRGH----DPMNAAMKTFETIAMAK 650
             +   +E YMGLVE GVGL+P GGG KE+ I  ++       DP     K F  IAMAK
Sbjct: 597 DAMNPYAETYMGLVEIGVGLLPAGGGTKEMAIRAIKLAEEYDMDPTPFIFKNFMNIAMAK 656

Query: 651 VSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASL---YDTGWRPPVKEKVKVPGET 707
           VS SA E  +M  +++ D ++++ D  ++DAK    +L   Y  G RP +   +K PG  
Sbjct: 657 VSMSAAELNQMGFMRQGDAVAMDMDTRIFDAKLKVIALAANYRPG-RPLI--DLKAPGRG 713

Query: 708 GYAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSL 767
             A++      M++ G+ISE+D  + K +A VI GG VP GT + E+YLLE+EREAF+ L
Sbjct: 714 IAASIKSQLWNMRMGGFISEYDEFLGKTIADVITGGDVPAGTLITEDYLLELEREAFVRL 773

Query: 768 SGEAKSQARMQHMLVKGKPLRN 789
            G+ K+  R+Q+ML KGK LRN
Sbjct: 774 CGQKKTLDRIQNMLKKGKTLRN 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: 1425
Number of extensions: 70
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: 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 Apr 09 2024. 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 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