GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Salinicoccus carnicancri Crm

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_017549143.1 C792_RS0108995 aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_000330705.1:WP_017549143.1
          Length = 501

 Score =  285 bits (730), Expect = 2e-81
 Identities = 174/489 (35%), Positives = 265/489 (54%), Gaps = 22/489 (4%)

Query: 37  YPLVINGERVETEAKIVS--INPADKEEVVGRVSKASQEHAEQAIQAAAKAFE--EWRYT 92
           Y L INGE+VE+     +  INPA  E V+ +V+ A+ E AE+A+ AA  AFE  +W+  
Sbjct: 15  YELFINGEKVESSDGGTNDIINPATGE-VIAKVAMATGEDAERAVMAARDAFENSKWKIY 73

Query: 93  SPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELA 152
              +RA +L R A+ +R R  E   L V  +GK  N A     +A++  EYYA  +    
Sbjct: 74  PASKRAKILNRIASIMRERFKELVELEVLNSGKSINAATGQINQAVEDFEYYAGAVCN-- 131

Query: 153 KGKPVNSREGEKNQYVYT-PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATP 211
            G   N   G+ + Y    P GV   I PWN+   + A      +  G TVVLKPAS TP
Sbjct: 132 HGGQTNDVPGQFHNYTEKEPVGVCAQIVPWNYPLMMAAWKVAPALAAGCTVVLKPASLTP 191

Query: 212 VIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAA 271
           + A    E+ +E+G+P GV+N +PGSG+ VGDYLV+HP+   + FTGS + G  I  +A+
Sbjct: 192 LTALILGEICQEAGVPDGVINILPGSGSRVGDYLVEHPEVDKVAFTGSTDTGKDIMSKAS 251

Query: 272 KVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEK 331
           +       LKR+  E+GGK   ++  DA++E A  S     +   GQ C A SR  V ++
Sbjct: 252 RT------LKRLTLELGGKSPALIFGDAELENAVASSVYGIYNNTGQSCDARSRIYVEDR 305

Query: 332 VYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEGRLVS-GGTG 390
           +YD+ +E+ +E T+      P S + +MG +ID+   + + +YIE  +QEG  ++ GG  
Sbjct: 306 IYDKFVEQFVEKTKQMKMGDPMSKETHMGSLIDKSQLESVEAYIETARQEGATIAYGGNR 365

Query: 391 DDSKGY----FIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTG 446
              +GY    +++PTI  D+     ++++EIFGPVV   + SD  EA+ +ANNT YGL  
Sbjct: 366 LSIEGYEGGFWLEPTIITDVTEDMTVVRDEIFGPVVVISRFSDEKEAVSLANNTIYGLAS 425

Query: 447 AVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHM 506
           ++ T + +  +R   +   G +    NC  +     PFGG+K SG   +    + L L+ 
Sbjct: 426 SIYTEDTRKAKRVADKIRAGIVMI--NCPFSAFPGTPFGGYKQSGFGRELSA-ETLDLYS 482

Query: 507 QAKTISEMF 515
           + K+I   F
Sbjct: 483 ETKSIMSYF 491


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: 601
Number of extensions: 29
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: 501
Length adjustment: 34
Effective length of query: 481
Effective length of database: 467
Effective search space:   224627
Effective search space used:   224627
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 24 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