GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Marinobacter adhaerens HP15

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate GFF3397 HP15_3339 acyl-CoA dehydrogenase domain protein

Query= SwissProt::P33224
         (541 letters)



>FitnessBrowser__Marino:GFF3397
          Length = 566

 Score =  447 bits (1149), Expect = e-130
 Identities = 240/523 (45%), Positives = 321/523 (61%), Gaps = 8/523 (1%)

Query: 5   THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64
           TH VFNQP  L N NL+  D AL EA  REGAG  ++ L + G   G A++++LG  AN 
Sbjct: 23  THEVFNQPPALENYNLFEQDIALQEAALREGAGKAAEDLKAFGALAGAAQTIDLGFRANA 82

Query: 65  NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124
           N P    +D  G R+D+V FHPA+H LM+    N +H+  W    + GA VARAA++ +H
Sbjct: 83  NKPVFNTHDRFGHRIDEVDFHPAYHELMRIAFDNGLHSSPWSHPGQ-GAHVARAAKYYMH 141

Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184
           +QVEA   CP+TMTFAA P + +  P    DW   +L+D YD   LP  QK  + IGM M
Sbjct: 142 SQVEAAHCCPVTMTFAAIPSIRKQ-PELAADWEARILADSYDPRNLPDSQKSSVTIGMAM 200

Query: 185 TEKQGGSDVMSNTTRAERLEDG----SYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFV 240
           TEKQGGSDV +N+TRA  +  G    +Y LVGHKWF S P  DA LVLAQT  GLSCF +
Sbjct: 201 TEKQGGSDVRANSTRAYPIGAGGPGQAYELVGHKWFVSAPMCDAFLVLAQTQSGLSCFLM 260

Query: 241 PRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTRF 300
           PR+ PDG +N  +++RLK+K+GN +NAS E E + A+ W++G EG G+  I++M  MTRF
Sbjct: 261 PRWRPDGTKNPWQVQRLKNKMGNVANASSEAELRGALAWMVGEEGRGVPTIIEMVAMTRF 320

Query: 301 DCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLAR 360
           DC +GS A MR+A + A +H   R  FG  LI QPLM++VL+ +AL+ E   A   R+AR
Sbjct: 321 DCMIGSSAGMRQAIAQASHHCRHRSAFGARLIDQPLMQNVLADLALESEAALAYTMRIAR 380

Query: 361 AWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPV 420
           A D +    E L ARL TP  K+ ICKR      EAME +GG G  E+  +PRL+RE PV
Sbjct: 381 ALDNQDKEHERLLARLATPVGKYWICKRTPNHAYEAMECIGGSGVMEDCIMPRLFRESPV 440

Query: 421 NSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLR--KPA 478
           N+IWEGSGN+ CLD LR L K+    D       E KG DR FD+ + +LQ         
Sbjct: 441 NAIWEGSGNVQCLDTLRALQKEPETLDAFFNEAAEAKGADRRFDQFLAQLQHDFADISDF 500

Query: 479 EELGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGGV 521
           +   R +  ++ L   G+ +L+++   +A A+C   L+  GG+
Sbjct: 501 QYRARNLVDRMALALQGSLLLRHSDAAVADAFCASRLEASGGM 543


Lambda     K      H
   0.324    0.138    0.428 

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: 681
Number of extensions: 28
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: 541
Length of database: 566
Length adjustment: 36
Effective length of query: 505
Effective length of database: 530
Effective search space:   267650
Effective search space used:   267650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 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