GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Streptomyces kebangsaanensis SUK12

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein

Query= curated2:Q9K5Z5
         (515 letters)



>NCBI__GCF_001906585.1:WP_073948994.1
          Length = 462

 Score =  240 bits (613), Expect = 7e-68
 Identities = 169/465 (36%), Positives = 226/465 (48%), Gaps = 27/465 (5%)

Query: 50  DKIVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEERANILIRAAAIIR 109
           D I  VNPA  EQVI  V   + E VD A ++A  A   W    P ERA  L     ++ 
Sbjct: 20  DAIEVVNPA-DEQVIATVPAGTAEDVDAAVRAARAALPGWAATPPAERAARLTALRDVLV 78

Query: 110 RRKHEFSAWLVKEAGKPWKEADADTAEA-IDFLEYYARQMITLKDGKPVNSREGEHNRYF 168
            RK E +  +  E G P   + A  A   I     YA    T    + V +    H    
Sbjct: 79  ARKDEIAETVTAELGSPLAFSQAVHAGVPIAVAGSYADLAATYAFEEKVGNSTVHHE--- 135

Query: 169 YTPIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVVAAKFVEVLEEAGLPK 228
             P+GV   I+PWN+ L  +       +  G T++LKPA  TP+ A  F E   EAG+P 
Sbjct: 136 --PVGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAEDTPLTAQLFAEAAHEAGIPA 193

Query: 229 GVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEMG 288
           GV+N V G G   G  L +HP   L++FTGS  VG R+   A         +KRV +E+G
Sbjct: 194 GVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVGRRIGATAGAA------VKRVALELG 247

Query: 289 GKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTKQLS 348
           GK   V+   ADL  A    V +    SGQ CSA +R ++H+D YD  +E  +A T    
Sbjct: 248 GKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYDEAVE--LAATAAAK 305

Query: 349 VGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGG-EGDDSKGFFIQPTIFADV 406
            G+       +GPVV+    +++  YIE G  EG RL+ GG E    KG+F+ PT+FADV
Sbjct: 306 YGD------RIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPEAPCEKGYFVSPTVFADV 359

Query: 407 DPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFHVG 466
            P   + QEEIFGPV++  +  D D AL IAN T YGL GAV   +        R    G
Sbjct: 360 TPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVWAADETEAVAFARRMDTG 419

Query: 467 NLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTV 511
            +  N    G      PFGG+K SG   + G    L  ++Q K++
Sbjct: 420 QVDIN---GGRFNPLAPFGGYKQSGVGRELGAHG-LTEYLQTKSL 460


Lambda     K      H
   0.318    0.135    0.394 

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: 541
Number of extensions: 22
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: 462
Length adjustment: 34
Effective length of query: 481
Effective length of database: 428
Effective search space:   205868
Effective search space used:   205868
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 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