GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudomonas fluorescens FW300-N2C3

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate AO356_07180 AO356_07180 aldehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07180
          Length = 481

 Score =  265 bits (678), Expect = 2e-75
 Identities = 163/472 (34%), Positives = 244/472 (51%), Gaps = 20/472 (4%)

Query: 35  KDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSP 94
           K +   ING+ V       +INP+D  +V+G  +KA       AI+AA  AF  W  +  
Sbjct: 5   KRFDNYINGQWVAGADYCTNINPSDLSDVIGEYAKADAAQVNAAIEAARAAFPAWSTSGI 64

Query: 95  EERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKG 154
           + R   L +  +++  R+ E   LL +E GK   EA  +   A +  +++A + + L+  
Sbjct: 65  QARHDALDKVGSEILARREELGQLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGD 124

Query: 155 KPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIA 214
              + R G   +      GV  +I PWNF  AI A      +  GN VV+KPA   P  A
Sbjct: 125 YVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCA 184

Query: 215 AKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGS----REVGTRIFERA 270
               E++  +G P G  N V GSG  VG+ LV+ PK   I+FTGS    R++      R 
Sbjct: 185 WALAEIISRAGFPAGAFNLVMGSGRVVGEVLVNSPKVDGISFTGSVGVGRQIAVNCVSRQ 244

Query: 271 AKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHE 330
           AKVQ           EMGGK+  ++ +DAD++ A +    SAF   GQ+C+A SR +V  
Sbjct: 245 AKVQ----------LEMGGKNPQIILDDADLKQAVELAVQSAFYSTGQRCTASSRLIVTA 294

Query: 331 KVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG- 388
            ++D+ +  + E  +S        A   +GPV+ +    + + YI+IG+ EG RLVSGG 
Sbjct: 295 GIHDKFVAAMAERMQSIKVGHALKAGTDIGPVVSEAQLSQDLKYIDIGQSEGARLVSGGG 354

Query: 389 -TGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGA 447
               D++GYF+ PT+FAD +   R+ +EEIFGPV    +V+D++ AL +AN+TE+GL+  
Sbjct: 355 LVTCDTEGYFLAPTLFADSEASMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAG 414

Query: 448 VITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGG 498
           + T + K+    K+    G +  N    G  V YH PFGG K S   S+  G
Sbjct: 415 IATTSLKYANHFKRHSQAGMVMVNLPTAG--VDYHVPFGGRKGSSYGSREQG 464


Lambda     K      H
   0.316    0.133    0.379 

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: 573
Number of extensions: 23
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: 515
Length of database: 481
Length adjustment: 34
Effective length of query: 481
Effective length of database: 447
Effective search space:   215007
Effective search space used:   215007
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 (21.6 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