GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Kocuria turfanensis HO-9042

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_062735451.1 AYX06_RS08775 aldehyde dehydrogenase family protein

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>NCBI__GCF_001580365.1:WP_062735451.1
          Length = 1178

 Score =  286 bits (733), Expect = 6e-81
 Identities = 323/1051 (30%), Positives = 446/1051 (42%), Gaps = 126/1051 (11%)

Query: 257  RLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEADAQRYLASYEQAINAIG 316
            RL+G   V         A  RK  A+G R + ++LGE  + + +A ++LA      +A  
Sbjct: 119  RLVGHMIVDARPKPFGQA-VRKLTAQGHRLNINLLGEEVLGQEEADKHLA------DAAA 171

Query: 317  QASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSLTLLARQYDIG---INI 373
               R    Y    +S+K+S++ P+ S    E  +  +  RL  +   A Q   G   IN+
Sbjct: 172  LLDRDDVDY----VSLKVSSVVPQLSHWGFEGTVAAVVERLLPVCRAAAQAPAGSKFINL 227

Query: 374  DAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDYLIDLARRSRHR-- 431
            D E    L ++ ++  RL   PEL G    G VVQ Y    P  +  +  L+  S  R  
Sbjct: 228  DMEVYSDLHLTTEVFTRLLERPELRGLEA-GIVVQAY---LPDALAVVRRLSAWSAERVA 283

Query: 432  -----LMIRLVKGAYWDSEIKRAQVDGLEGYPVYT--RKVYTDVSYVACARKLLSVPDVI 484
                 + +RLVKGA    E   A+   L G+P+ T   K  TD +Y    +++L    V 
Sbjct: 284  AGGAGIKVRLVKGANLPMERVDAE---LHGWPLATWGTKQDTDTNY----KRVLDW--VF 334

Query: 485  YPQ--------FATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGK 536
             P+         A HN   +A  + +A       + EF+ L GM       V   + +  
Sbjct: 335  RPERMSGLRLGVAGHNLFDIAFAHLLAQRRGVTERIEFEMLQGMAVEQARAVSADVGE-- 392

Query: 537  FNRPCRIYAPV---GTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVE 593
                  +Y P       +  ++YLVRRL EN ++ +F++ I D     +    +      
Sbjct: 393  ----LLLYVPAVRPAEFDVAVSYLVRRLEENASHENFMSGIFDLAPDNEVFAREERRFRA 448

Query: 594  QMHA-DEGALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAV 652
             + A D      P P  AQ R+  G   A S  + L    R    +   +         +
Sbjct: 449  ALEALDPRQDADPVPARAQDRSAPG---AGSEHLPLDEAFRNEPDTDVAVPANQAWAEGI 505

Query: 653  PLLGTEAAAGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPAD 712
                T+    E++  P PV                  A+VE  +     AA  W A  A 
Sbjct: 506  AARITDRRWYEELPVPGPV----------------DAADVERLVATGRAAAEDWHARGAR 549

Query: 713  VRAAALERAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSD 772
             RA  L RAA+++ A+   L+ +   EAGKT   +  EV EAVDF R+YA +  E  + D
Sbjct: 550  ERAEILNRAADVLAARRAHLLAVAGAEAGKTLGQSDPEVSEAVDFCRWYARRALELETVD 609

Query: 773  THR--PLGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAG 830
              R  P   V+   PWNFPLAI TG   AALAAG  VL KPA +    +   V  L EAG
Sbjct: 610  GARFVPDRLVLVTPPWNFPLAIPTGSTVAALAAGAAVLHKPAPEVRRCSTAVVEALWEAG 669

Query: 831  VPAGAVQLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIA 890
            VP   +QL+      VG ALV    V  ++ TG+ E A+L      GR        PL A
Sbjct: 670  VPRDVLQLVDSVEGEVGQALVSHPGVDRIVLTGAYETAQLFGSWRPGR--------PLTA 721

Query: 891  ETGGQNAMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVA--DRVLEMLKGA 948
            ET G+NAM++  SA  ++ V D+V SAF  AGQ+CSA  +  L   VA   R    L  A
Sbjct: 722  ETSGKNAMVITPSADRDRAVWDLVTSAFGHAGQKCSAASLGILVGSVARSPRFRRQLLDA 781

Query: 949  MDELTMGNPDRLSTDVGPVIDEEARGNIVR---HIDAMRAKGRRVHQADPNGAL-----S 1000
               + +  P  L   VGP IDE   G + R    +D          Q D  G L      
Sbjct: 782  ASSMVVDWPQNLQATVGPTIDEPG-GKLRRALTRLDPGEEWLLEPRQLDDTGRLWRPGIK 840

Query: 1001 AACRNGTFVSPTLIELDSIEELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIH 1060
                 G+F   T            E FGPVL ++    + L   L   N   YGLT G+H
Sbjct: 841  TGVAPGSFYHRT------------ECFGPVLGLME--ASDLHEALELQNAVHYGLTAGLH 886

Query: 1061 TRIDETIEHIVERAEVGNLYVNRNIVGAVVGVQPFGGEGLS--GTGPKAGGPLYLHRLLS 1118
            +   E I   V+  E GNLYVNR I GA+V  QPFGG   S  G G KAGGP YL +L S
Sbjct: 887  SLDPEEISTWVDLVEAGNLYVNRGITGAIVQRQPFGGWKRSSVGLGAKAGGPNYLVQLGS 946

Query: 1119 VCPLDAVARVVRASDTVGGADETGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAA 1178
                 A    V A  +  GA   GP+       L  L+       AA     A  ++   
Sbjct: 947  W--QKAPFAEVPAGQSGTGARPAGPI----AHHLEALRPLVPEADAAWLTACAEQDQAWW 1000

Query: 1179 ASAAGLSVTLPGPTGERNTYTLLPRAAVLCLAQQE--TD-LAVQLAAVLAAGSQAVWVES 1235
                G      G   E N +   PR  V+  A+    TD + V LAAV +  S+AV V +
Sbjct: 1001 EREFGRVHDASGLACEANLFRYRPRDVVVRAAEDAPLTDVIRVGLAAVRSC-SRAVLVPA 1059

Query: 1236 P----MARALFARL--PKAVQSRVRLVADWS 1260
                   R LF  +  P   ++  R+ ADWS
Sbjct: 1060 AEVPGEVRELFRSVLDPCGDEAFARVAADWS 1090


Lambda     K      H
   0.318    0.133    0.383 

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: 3198
Number of extensions: 153
Number of successful extensions: 10
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: 1333
Length of database: 1178
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1130
Effective search space:  1452050
Effective search space used:  1452050
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 (21.7 bits)
S2: 59 (27.3 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