Alignments for a candidate for fadB in Salinicoccus carnicancri Crm

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Salinicoccus carnicancri Crm

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_017549210.1 C792_RS0109330 enoyl-CoA hydratase/isomerase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000330705.1:WP_017549210.1
          Length = 752

 Score =  411 bits (1056), Expect = e-119
 Identities = 269/792 (33%), Positives = 411/792 (51%), Gaps = 49/792 (6%)

Query: 5   IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64
           IRKA VLG+GVMGS IAA L N G+ V +LDI  +                +  + +S++
Sbjct: 3   IRKATVLGAGVMGSQIAALLVNAGLRVKILDIAGD---------------RDEPNEISKK 47

Query: 65  AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVDE 124
           A   +  +K   L      S +T GN E+D       D  IE V E+L +K +++  V  
Sbjct: 48  AYDTITDKKRPQLFDLSFASNLTYGNFEEDLTGDDGTDIYIEAVKEDLGIKHEVWDKVRR 107

Query: 125 HRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDIL 184
                ++ ++NTSGI +  +++   D  K  F G HFFNP R +KL+E+IP   T  D L
Sbjct: 108 TAGDRTLFATNTSGIPIASISKVFDDSEKKRFFGMHFFNPPRIMKLVEVIPYANTSSDAL 167

Query: 185 KFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLIG 244
           + +  F E+VLGKGVV A D P F+ANRIGT  +   +    + G+ + E D++TG  IG
Sbjct: 168 EEVQLFLEDVLGKGVVIANDVPAFVANRIGTQTMNDIMFRAEQQGFSIAETDALTGRNIG 227

Query: 245 RPKSATFRTLDVVGLDTFAHVARNVYDKADGDEKEVFRIPSFMNDMLEKGWIGSKAGQGF 304
           RP + T+  +D+VGLD    V R +  +   +EK+ F        ++EKG  G K  QGF
Sbjct: 228 RPGTGTYGLVDLVGLDIAVTVIRGL--QQIPEEKQFFHDTKIAGTLMEKGAFGKKKKQGF 285

Query: 305 YKKEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGRLLWNIT 364
           YKK  +     DP +  Y    + +   L   K  +   A + A+  ++D AGR LW   
Sbjct: 286 YKKGKEDYLVFDPESNDYITPDQPEFHIL--GKFGRDLGANLDAVFNAEDEAGRFLWETL 343

Query: 365 SQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQLGADMPG 424
                YSA  + + A D   ID+AM WGF W+ GPF++WD +G ++  E++E    ++PG
Sbjct: 344 RNNFYYSALNVPKAASDYADIDRAMVWGFNWKKGPFQLWDMMGFERVKERMENELGELPG 403

Query: 425 WIKEMLDKGNETFYIKENGTVFYYDRGEYRAVKENKKRIHLQALKETKGVIAKNSGASLI 484
           W             IK+  T FY +      V            + T   I     + L 
Sbjct: 404 W-------------IKKRDTPFYSESDSIERV--------TPVSEFTDSEIWNREDSLLS 442

Query: 485 DLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETE-RNYKGLVIGNQGKNFCVGANLAMIL 543
               D  LL+  S++N I  D    + + ++  E  +Y  +VI  +G++F VGA+L  ++
Sbjct: 443 VAHSDQLLLKLQSRNNIISDDFAGDLIESIDLLENEDYSSMVIYAEGRHFSVGADL-YLM 501

Query: 544 MEVQDDNFLE--VDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARIQAAS 601
            ++ +DN +E  V   I +  E+  ++KY+ KPVV A +G +LGGG E  L +  + AAS
Sbjct: 502 KKMHEDNRVEEIVGPAIDKLHESFNRLKYALKPVVTAVYGKSLGGGCELVLHSPIVVAAS 561

Query: 602 EAYMGLVESGVGLIPGGGGNKELYINHLRRGH---DPMNAAMKTFETIAMAKVSASAQEA 658
           E YMGLVE+GVGL+P GGG  E+    L  GH   D      +    IA AKVS +A EA
Sbjct: 562 ETYMGLVEAGVGLVPSGGGLAEMADRILSTGHMQNDKQKTMTEVMTNIAFAKVSTNAHEA 621

Query: 659 REMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAALLLG-AE 717
            +   L+ TD I +N +  +  A + A    +T + P  K      G   Y AL  G  +
Sbjct: 622 LKYKYLRNTDTIILNAEKRVEIALERARYESETNYIPKPKVNYTALGR-DYKALAKGQLD 680

Query: 718 QMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAKSQARM 777
             +   +IS++D+++   +A+V++GG++P  T +++ Y+ ++E+E FL+L    K+  R+
Sbjct: 681 AQRTGNFISDYDYEVTLDVAHVLSGGELPRNTIINQGYIQKLEKERFLTLLQNDKTYNRI 740

Query: 778 QHMLVKGKPLRN 789
           +HML  GKPLRN
Sbjct: 741 KHMLETGKPLRN 752


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: 1315
Number of extensions: 58
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: 752
Length adjustment: 41
Effective length of query: 748
Effective length of database: 711
Effective search space:   531828
Effective search space used:   531828
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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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