GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Sphingomonas koreensis DSMZ 15582

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::P94391
         (515 letters)



>FitnessBrowser__Korea:Ga0059261_3374
          Length = 474

 Score =  220 bits (560), Expect = 1e-61
 Identities = 152/478 (31%), Positives = 242/478 (50%), Gaps = 24/478 (5%)

Query: 41  INGERVETEA--KIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERA 98
           I GE VE+E   +   INPA  E  V  ++  S+  A++A+ AA  AF+ +  TS +ER 
Sbjct: 9   IGGEWVESEGGTRHDVINPAT-EAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVDERI 67

Query: 99  AVLFRAAAKVRRRKHEFSALLVKEAGKPWNEAD-ADTAEAIDFMEYYARQMIELAKGKPV 157
           A+L    A+ + R  + +  +  E G P + A  A     I  +       I   K    
Sbjct: 68  ALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHL----MSTINALKAFEF 123

Query: 158 NSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKF 217
           + + G+ +  V+ P GV  +I PWN+    +       +  GNT+VLKP+   P  AA F
Sbjct: 124 SEQIGQ-SLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAAIF 182

Query: 218 VEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQ 277
            E+++++G+P GV N V G G  VG  L  H    +++FTGS   G ++ + AA+     
Sbjct: 183 AEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAET---- 238

Query: 278 QHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVL 337
             +KRV  E+GGK   V+   AD+  A Q    S    +GQ C A +R +VHE    +  
Sbjct: 239 --VKRVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAA 296

Query: 338 ERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD---S 393
           +    + ++  T  P     ++GPV+++  ++KI   I  G +EG +L +GG G      
Sbjct: 297 QIASGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIE 356

Query: 394 KGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNR 453
            GYF+KPT+F+ +     + +EEIFGPV+      D +EA+ +AN+T+YGL+ AV+  + 
Sbjct: 357 TGYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLS-AVLFGSP 415

Query: 454 KHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTI 511
           + ++R       G +Y N       +   PFGG+K SG + +  G   LA  M+ K +
Sbjct: 416 EEVKRVAPRLRAGMVYINGGQPDPSL---PFGGYKQSG-NGREHGKFGLAEFMEVKAM 469


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: 607
Number of extensions: 33
Number of successful extensions: 5
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: 474
Length adjustment: 34
Effective length of query: 481
Effective length of database: 440
Effective search space:   211640
Effective search space used:   211640
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