GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Echinicola vietnamensis KMM 6221, DSM 17526

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::P94391
         (515 letters)



>FitnessBrowser__Cola:Echvi_0481
          Length = 509

 Score =  209 bits (531), Expect = 2e-58
 Identities = 155/475 (32%), Positives = 234/475 (49%), Gaps = 36/475 (7%)

Query: 32  YLGKDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRY 91
           ++G  +   ++GE  +       I+P D + V  +V++      E A+ AA KAF  W  
Sbjct: 25  FIGGKFVPPVDGEYFDV------ISPVDGQ-VFTKVARGKAADIELALDAAHKAFPAWSR 77

Query: 92  TSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYARQMIE 150
           TS  ER+ +L + A ++  +    +A+   + GKP  E  +AD A  +D   Y+A  +I 
Sbjct: 78  TSATERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAG-VIR 136

Query: 151 LAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAP-IVTGNTVVLKPASA 209
             +G      +   +  V  P G+   I PWNF   +MA   +AP +  G   ++KPA  
Sbjct: 137 AEEGSIAELDQHTVSVNVKEPIGIVGQIIPWNFPM-LMATWKMAPALAAGCCTIVKPAEQ 195

Query: 210 TPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFER 269
           TP      +EV+ +  LP GV+N V G G E G  L   P+   + FTG    G  I + 
Sbjct: 196 TPASIMILMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQY 254

Query: 270 AAKVQPGQQHLKRVIAEMGGKDTVVVDE---DADIELAAQSIFTSAFGFA---GQKCSAG 323
           A+      ++L  V  E+GGK   V      DAD E   + +   A  FA   G+ C+  
Sbjct: 255 AS------ENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCL-EGAVMFALNQGEVCTCP 307

Query: 324 SRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEGR 383
           SR +VHEK+YD  +E+VI   E+     P      MG    +  ++KI+SYI+IGKQEG 
Sbjct: 308 SRILVHEKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGA 367

Query: 384 LVSGGTGDDSK-------GYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEV 436
            V  G G+ +K       GY++KPT+    + K R+ QEEIFGPV +     D +EA+ +
Sbjct: 368 EVLTG-GEVAKLNSGLENGYYVKPTLLKGHN-KMRVFQEEIFGPVCSVATFKDVEEAISI 425

Query: 437 ANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491
           +N+T YGL   V T +     +  +    G ++   NC  A   + PFGG+K SG
Sbjct: 426 SNDTLYGLGAGVWTRDAHEAYQVPRAIKAGRVWV--NCYHAYPAHAPFGGYKKSG 478


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: 602
Number of extensions: 37
Number of successful extensions: 6
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: 509
Length adjustment: 35
Effective length of query: 480
Effective length of database: 474
Effective search space:   227520
Effective search space used:   227520
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