GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Marinicella litoralis KMM 3900

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_099019966.1 CCS90_RS12790 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_002591915.1:WP_099019966.1
          Length = 788

 Score =  760 bits (1963), Expect = 0.0
 Identities = 404/805 (50%), Positives = 532/805 (66%), Gaps = 25/805 (3%)

Query: 6   VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPAPLGI 65
           ++KVA+LGAGVMGAQIAAH  NA +P +LFDL AKEGPKNGI  +A+  LKKL PAPLG 
Sbjct: 6   IRKVAILGAGVMGAQIAAHFANAGIPALLFDLAAKEGPKNGIVNKALAGLKKLKPAPLGD 65

Query: 66  KEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATNTSGL 125
                LI+ ANY+DD+  LK+ DL+IEA+AERMD K  +Y  V  ++   AIFATNTSGL
Sbjct: 66  SAVLSLIEPANYQDDLEKLKQADLIIEAVAERMDIKKSVYDMVEDYINQDAIFATNTSGL 125

Query: 126 SITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTLGKGV 185
           SI  L+    A L+S+FCGVHFFNPPRYMHLVE+IPT  T  +++  LE  LTT +GKGV
Sbjct: 126 SINELATVLPASLQSKFCGVHFFNPPRYMHLVEIIPTNNTDDKVVSDLETVLTTVVGKGV 185

Query: 186 VRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTADVVGL 245
           V AKDTPNFIANR+G+FSI++      +FGIPF+ +D LTG+ +GR KSATFRTADVVGL
Sbjct: 186 VIAKDTPNFIANRIGVFSIVSTMHHGAEFGIPFETIDALTGTLIGRPKSATFRTADVVGL 245

Query: 246 DTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKVLDAK 305
           DT+AH I TM++ L DDP+   ++ P  +K L+D GALGQKT AG Y K+G+ I VLD  
Sbjct: 246 DTLAHTINTMKNGLPDDPWHAHFEQPVWMKALIDKGALGQKTRAGVYMKKGRDILVLDTD 305

Query: 306 TGQYVDAGKKADEIVVRMLKK-DAAERIKLLREST-NPQAQFLWAVFRDVFHYIAVYLEQ 363
            G+Y       D  VV ++KK    +R+  L   T +PQAQFLW++FRD+FHY A  LE 
Sbjct: 306 KGEYRAQNAALDPRVVEIMKKGKPQDRLTELHALTDSPQAQFLWSIFRDLFHYCATQLEH 365

Query: 364 IAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWVFEG 423
           IA +A DID AIRWGFG+  GPFE WQ++GW ++   + +D++AGK ++++P+P+WV   
Sbjct: 366 IADTARDIDFAIRWGFGYGQGPFETWQASGWNRIVSMIVDDIDAGKTMASSPMPSWVM-- 423

Query: 424 PVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEENDA 483
              +  G H A GS+S A  SF  RS   VYQRQ F   +     ++    G T+ E+D 
Sbjct: 424 ---KVDGAHGAEGSYSAAEDSFKPRSTAAVYQRQLFPDRL----ISEQAHYGETIFEDDD 476

Query: 484 VRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLGAPG 543
           +R+W     D++ + SFK+K + I   V+ GL +A+ +AE  YKGL+VWQ          
Sbjct: 477 IRVW--HQGDEIAIASFKTKKHIIAEGVLKGLRKAVSIAEKDYKGLIVWQTEE------- 527

Query: 544 GPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGGCEL 603
            PF+ GANL  A  A   G    +E  V  FQ     ++++SVP + A  G+ALGGGCE 
Sbjct: 528 -PFTLGANLAPAAMAISAGQVDAVEQSVDFFQQTSQTLRFSSVPTIMATRGMALGGGCEF 586

Query: 604 MLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSRFQS 663
            + + S VAA ETYIGLVE GVGL+PAGGGLKE    A R A+ +   ++   L   F+ 
Sbjct: 587 SMSATSVVAAFETYIGLVEAGVGLLPAGGGLKE---IARRTAKESFGKDLYPMLEHYFKK 643

Query: 664 AAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPL-PTLVPVA 722
            AMA V+ SALEA+Q+G+L+P  +IVFN +E+LYVA+ +V+ L   GY AP     + VA
Sbjct: 644 VAMAAVAGSALEAKQIGFLKPCTEIVFNPNEILYVAKAKVKYLHDKGYTAPANEQNIRVA 703

Query: 723 GRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALERKAF 782
           G   IA ++  L NM +G  IS HD+ IA RIA  + GG V++ SLV+E +LL LERK F
Sbjct: 704 GEPAIANMEMMLANMIEGNMISEHDYEIAKRIAIVMAGGFVDSDSLVTEQYLLDLERKYF 763

Query: 783 VDLLGTGKTQERIMGMLQTGKPVRN 807
           ++L+   KT  RI   L TGKP+RN
Sbjct: 764 MELIQMPKTLARIEHTLTTGKPLRN 788


Lambda     K      H
   0.319    0.134    0.391 

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: 1347
Number of extensions: 56
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: 807
Length of database: 788
Length adjustment: 41
Effective length of query: 766
Effective length of database: 747
Effective search space:   572202
Effective search space used:   572202
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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