GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Marinobacter adhaerens HP15

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Marino:GFF3684
          Length = 489

 Score =  258 bits (659), Expect = 3e-73
 Identities = 168/484 (34%), Positives = 254/484 (52%), Gaps = 16/484 (3%)

Query: 2   AEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWS 61
           A +  ++N+++G ++ + T +   VVNPAT +V+ +V ++ +     A ++A   F  WS
Sbjct: 3   ASLPVVQNFVHGRFLANSTGETFPVVNPATGQVIYEVEVADESVQQAAIESARAGFAEWS 62

Query: 62  KVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALG-EVGRGIENVEFAAGAPS 120
            +    R+RIL     +L +  +ELA     + GK  +EA   +V  G + VEF AG   
Sbjct: 63  AMTAIERSRILLRAVAILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAG--- 119

Query: 121 LMMGDSLASIATDVEAANY---RYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKP 177
             +  S+     D+    Y   R P+G+  GI  +N+P+ + CW    A+A GN  I KP
Sbjct: 120 --LAPSIEGNQQDLGGDFYYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKP 177

Query: 178 SERTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVY 237
           SE TP+   KL E+F +AG+P GVFNVV GA +V   +  HPEI  +SF G    G+ V 
Sbjct: 178 SEETPMGAVKLAEIFTEAGVPAGVFNVVQGAAEVGQWLTHHPEIAKVSFTGEVATGKKVM 237

Query: 238 KKGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIA 297
              S  LK V    G K+  I+ +DA+LE+ ++  +   F + GE C     V V E + 
Sbjct: 238 AAASSTLKDVTMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLY 297

Query: 298 DEFMAKLQEKVA-DIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGREN 356
             F+ +L E+   +IK G+ ++     G +I   ++   L YI KGL EGA L   GR  
Sbjct: 298 PRFIERLLERTRNNIKPGDPMNPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAF 357

Query: 357 VSDD---GYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGAC 413
             +D   GYFV PTIF + T +MTI K+EIF PV+SV+  ++  E I  AN ++    A 
Sbjct: 358 EPEDSKGGYFVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAG 417

Query: 414 LFTSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTR 473
           +FT++          I AG+  IN    +P A  P  G+K S  G    NG++++  YT+
Sbjct: 418 VFTNDIRRAHRVIHQIQAGICWINSYGASP-AEMPVGGYKLSGIG--RENGRETIAHYTQ 474

Query: 474 KKVV 477
            K V
Sbjct: 475 IKSV 478


Lambda     K      H
   0.318    0.136    0.396 

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: 562
Number of extensions: 30
Number of successful extensions: 4
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: 487
Length of database: 489
Length adjustment: 34
Effective length of query: 453
Effective length of database: 455
Effective search space:   206115
Effective search space used:   206115
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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