GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Marinobacter adhaerens HP15

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein

Query= reanno::WCS417:GFF827
         (481 letters)



>FitnessBrowser__Marino:GFF964
          Length = 505

 Score =  288 bits (738), Expect = 2e-82
 Identities = 181/477 (37%), Positives = 268/477 (56%), Gaps = 11/477 (2%)

Query: 10  YING--QWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPA--WSTSGIQ 65
           Y+NG  QW A  +   +++P +  + +   A  D +  + A+ AARAAF A  WS     
Sbjct: 30  YLNGTYQWAANGEAFTSVSPIDGRE-LASIASCDQSDADQAVMAARAAFEAGIWSQLAPA 88

Query: 66  ARHDALDKVGSEILARREELGTLLAREEGKTLPEAIG-EVTRAGNIFKFFAGECLRLSGD 124
            R   L +    I A  +EL  L   + GK +  A   +V       ++ A    ++ G+
Sbjct: 89  KRKAVLLRFAELIEAHGDELALLETLDMGKPINHASNVDVPATARAIRWTAEAIDKVYGE 148

Query: 125 YVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCA 184
             P+    + + ++RE +GVV  I PWNFP+ + AWKIAPALA GN V++KP+E  P  A
Sbjct: 149 LAPTPHNQIGM-ISREPMGVVAAIVPWNFPMIMAAWKIAPALATGNSVILKPSEKSPLSA 207

Query: 185 WALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSC-VSR 243
             LA +   AG PAGVFN++ G G  VG  L     VD + FTGS  V +Q+ +    S 
Sbjct: 208 IRLAALAGEAGVPAGVFNVLPGYGHTVGKALALHMDVDCLVFTGSTNVAKQLMIYAGQSN 267

Query: 244 QAKVQLEMGGKNPQIILDDA-DLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVA 302
             +V LE GGK+P I+  DA DLK+A   +  +  ++ G+ CTA SRL+V   I  +FV 
Sbjct: 268 MKRVWLEAGGKSPNIVFADAPDLKKAAAEAASAIAFNQGEVCTAGSRLLVENSIRAEFVR 327

Query: 303 AMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEG 362
            + E +K+ + GH L   T  G +V QAQLD+ + YI IGQSEGARLV GG  +  +T G
Sbjct: 328 LICEALKTWRPGHPLDPATTCGAIVDQAQLDRIIDYIGIGQSEGARLVEGGQRILENTGG 387

Query: 363 YYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKY 422
            ++ PT+F      MRI+ EEIFGPV +V+     + A+A+AND+ +GL+A + T+++  
Sbjct: 388 LFVQPTVFDGVNNQMRIASEEIFGPVLSVIGFDTADEAVAIANDSIYGLAAAVWTSNINT 447

Query: 423 ANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479
           A+   +  +AG V +N    G D   PFGG K S  G R++  +A + YT +K +++
Sbjct: 448 AHKVAKALRAGSVWINHYDGG-DMTAPFGGFKQSGNG-RDKSVHAFDKYTELKATWL 502


Lambda     K      H
   0.318    0.134    0.390 

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: 500
Number of extensions: 20
Number of successful extensions: 3
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: 481
Length of database: 505
Length adjustment: 34
Effective length of query: 447
Effective length of database: 471
Effective search space:   210537
Effective search space used:   210537
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