GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaB in Caulobacter crescentus NA1000

Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= uniprot:Q92L07
         (510 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03243 CCNA_03243 NADP+-dependent
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
          Length = 499

 Score =  164 bits (415), Expect = 7e-45
 Identities = 150/489 (30%), Positives = 234/489 (47%), Gaps = 30/489 (6%)

Query: 10  VASEAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFR-- 67
           +A  + A++D  G   +  +G    + SP  G+ +  +    A +    +  A  AF   
Sbjct: 17  LAPPSQAVID--GDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDG 74

Query: 68  AWR-LVPAPKRGELVRLLGEELRAFKAD-LGRLVSIEAGKIPSEGLG-EVQEMIDICDFA 124
            WR   P  K+  L RL   EL    AD L  L S++ GK  S+    ++   I+ C + 
Sbjct: 75  RWRDQGPRQKKAVLFRLA--ELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWY 132

Query: 125 VGLSRQLYGLTIATERPGHRMMETWH-PLGVVGIISAFNFPVAVWSWNAALALVCGDAVV 183
                ++YG  + T  P  R+    H PLGV+G I  +NFP+ +  W  A AL  G++VV
Sbjct: 133 AEALDKVYG-EVGTS-PADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVV 190

Query: 184 WKPSEKTPLTALACQAILERAIARFGDAPEGLSQVLIGDRAI-GEVLVDHPKVPLVSATG 242
            KP+E++PLTAL   A+   A       P G+  V+ G   + GE L     V +++ TG
Sbjct: 191 LKPAEQSPLTALKLGALALEA-----GLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTG 245

Query: 243 STRMGREVGPRLAK-RFARAILELGGNNAGIV---CPSADLDMALRAIAFGAMGTAGQRC 298
           S  +GR +    A+    R  LELGG +  IV   CP  DL+ A +A A+G     G+ C
Sbjct: 246 SGPVGRRLMEYSARSNLKRVSLELGGKSPQIVFADCP--DLEAAAQAAAWGVFYNQGEVC 303

Query: 299 TTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKN 358
           T   RL V   + D  + R+ +  + + VG+PL+ +   G +V +   +     IA A +
Sbjct: 304 TAASRLLVEAPIKDAFLARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADS 363

Query: 359 HGG-AVTGGERVELGHENGYYVKPALVEMPKQEGPVL-EETFAPILYVMKYSDFDAVLAE 416
            G   V GG+RV      G+YV+P + +  + +  +  EE F P+L VM +S  D  +  
Sbjct: 364 QGARRVLGGQRVR-QEAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRL 422

Query: 417 HNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRE 476
            N    GL++ ++T D+ ++ R   A     G+  VN G    +I   FGG K++G GR+
Sbjct: 423 ANDTVYGLAAGLWTADVSKALR--GARRLKAGLVWVN-GWDACDITMPFGGFKQSGFGRD 479

Query: 477 SGSDAWKAY 485
               A   Y
Sbjct: 480 RSLHALHKY 488


Lambda     K      H
   0.317    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: 580
Number of extensions: 37
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: 510
Length of database: 499
Length adjustment: 34
Effective length of query: 476
Effective length of database: 465
Effective search space:   221340
Effective search space used:   221340
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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