GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Marinobacter adhaerens HP15

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein

Query= BRENDA::Q4DRT8
         (561 letters)



>FitnessBrowser__Marino:GFF964
          Length = 505

 Score =  140 bits (354), Expect = 9e-38
 Identities = 134/442 (30%), Positives = 202/442 (45%), Gaps = 32/442 (7%)

Query: 89  QKAIDTALQASRE------WSQTSFRDRAAIFLHAAHLISTKYRHELRAATMLGQSKSPF 142
           Q   D A+ A+R       WSQ +   R A+ L  A LI   +  EL     L   K   
Sbjct: 63  QSDADQAVMAARAAFEAGIWSQLAPAKRKAVLLRFAELIEA-HGDELALLETLDMGKPIN 121

Query: 143 QAEIDVIAESCDFLRFSVHYAENLYRDQPLSPSSGAVWNSLDYRPLEGFVSTIAPFNFAA 202
            A    +  +   +R++    + +Y +  L+P+       +   P+ G V+ I P+NF  
Sbjct: 122 HASNVDVPATARAIRWTAEAIDKVYGE--LAPTPHNQIGMISREPM-GVVAAIVPWNFPM 178

Query: 203 IAANLVACPALM-GNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFLPCEPDVMTNFV 261
           I A     PAL  GN V+ KPS  + LS   L  +  EAG+PAGV N LP     +   +
Sbjct: 179 IMAAWKIAPALATGNSVILKPSEKSPLSAIRLAALAGEAGVPAGVFNVLPGYGHTVGKAL 238

Query: 262 NSHRDLAGVAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHLVHPSA-DLKLA 320
             H D+  + FTGST V   +   IYA      N+ R+  E GGK  ++V   A DLK A
Sbjct: 239 ALHMDVDCLVFTGSTNVAKQL--MIYA---GQSNMKRVWLEAGGKSPNIVFADAPDLKKA 293

Query: 321 AALTVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDDFKSFMCAVID 380
           AA         QG+ C+A SRL    S   E    +    +  + G P D  +   A++D
Sbjct: 294 AAEAASAIAFNQGEVCTAGSRLLVENSIRAEFVRLICEALKTWRPGHPLDPATTCGAIVD 353

Query: 381 ETAFERNKKYIDIAKSSPSTYSVIAGGG--YDKTEGWFVQPTIVESKDSQAQLMHEEIFG 438
           +   +R   YI I +S  +   ++ GG    + T G FVQPT+ +  ++Q ++  EEIFG
Sbjct: 354 QAQLDRIIDYIGIGQSEGA--RLVEGGQRILENTGGLFVQPTVFDGVNNQMRIASEEIFG 411

Query: 439 PILTVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLRYAAGNYYI 498
           P+L+V  +D       +D    +   + Y L  +++  +         K LR  AG+ +I
Sbjct: 412 PVLSVIGFDT------ADEAVAIANDSIYGLAAAVWTSNINTAH-KVAKALR--AGSVWI 462

Query: 499 NDKCTGAVVGQQPFGGARASGS 520
           N    G +    PFGG + SG+
Sbjct: 463 NHYDGGDMTA--PFGGFKQSGN 482


Lambda     K      H
   0.320    0.133    0.402 

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: 627
Number of extensions: 38
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: 561
Length of database: 505
Length adjustment: 35
Effective length of query: 526
Effective length of database: 470
Effective search space:   247220
Effective search space used:   247220
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: 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