GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhizobium grahamii CCGE 502

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_016552585.1 RGCCGE502_RS02470 long-chain fatty acid--CoA ligase

Query= metacyc::MONOMER-20125
         (556 letters)



>NCBI__GCF_000298315.2:WP_016552585.1
          Length = 566

 Score =  149 bits (376), Expect = 3e-40
 Identities = 157/563 (27%), Positives = 240/563 (42%), Gaps = 82/563 (14%)

Query: 20  LERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYE 79
           LE++   Y + T+      + T+     +   +A+ + S+G+E G  V+V+ PNV Q   
Sbjct: 41  LEKSCARYANRTAFSSMGKTLTYGALESQTRKIAAWLQSIGLEKGDRVAVMMPNVLQNPV 100

Query: 80  LHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVP 139
             + +  AG ++  VN     R +   L  S +K IFV        LE  A   +Q  V 
Sbjct: 101 AVYGILRAGFVVVNVNPLYTPRELEHQLRDSGAKAIFV--------LENFARTVEQVLVK 152

Query: 140 ---RLVFMADESESGNSSELGKEFFC----------------SYKDLIDRG-DPDFKWVM 179
              R V +    E   +  L                      ++K ++  G     K   
Sbjct: 153 TDVRHVVVTSLGEMLGAKGLIVNLLVRRVKKLVPSWSIPQHKTFKQVLGEGAGKSLKPAS 212

Query: 180 PKSEWDPMILNYTSGTTSSPKGVVHCHRGIFI--MTVDSLIDWGVPKQPV-----YLWTL 232
            K + D   L YT GTT   KG V  HR +    + ++  +     K+P      +L  L
Sbjct: 213 LKGD-DIAFLQYTGGTTGIAKGAVLTHRNLLSNKLQLELWLQSAFDKKPRPEVLNFLCAL 271

Query: 233 PMFHANGWSYPWGMA-AVGGTNICLRKFDSEIIYDMIKRHG---VTHMCGAPVVLNMLSN 288
           P++H    +    M  ++G  NI +   +   I  ++K  G   V    G   + N L N
Sbjct: 272 PLYHIFALTVNSLMGMSLGAHNILVA--NPRDIPALVKEFGKVKVHIFPGLNTLFNALMN 329

Query: 289 APGSEPLKTTVQIMTAGA----PPPSAVLFRTESLGFAVSHGYGLTETAGLVVSCAWKKE 344
                 L  +  +M+ G       P A  +  +  G  ++ GYGL+ET+           
Sbjct: 330 NADFAKLDFSNIVMSLGGGMAVQRPVAERWM-KITGSHITEGYGLSETS----------- 377

Query: 345 WNHLPATERARLKSRQGVGTV----MQTKIDVVDPVTGAAVKRDGSTL-----GEVVLRG 395
               P     R  S +  G++      T++D+ D         DG++L     GE+ +RG
Sbjct: 378 ----PVATANRFDSAEFTGSIGLPLPSTELDIRD--------EDGNSLPLGEIGEICIRG 425

Query: 396 GSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEV 455
             VM GY   PE TA+ MT+DG+F +GD+G M   GY +I DR KD+I+  G N+   E+
Sbjct: 426 PQVMAGYWNKPEETARVMTSDGYFRSGDMGFMDARGYTKIVDRKKDMILVSGFNVYPNEI 485

Query: 456 ESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVP 515
           E +   HP ILEAA V  PD   GE    FV  K       TE ++  +C + L  Y  P
Sbjct: 486 EEVAAMHPGILEAAAVGIPDGHSGEAVKLFVVRKDPAL---TEADVKAHCAANLTNYKRP 542

Query: 516 KTVVFKEELPKTSTGKVQKFILR 538
           + V F+ ELPKT  GK+ +  LR
Sbjct: 543 RFVEFRTELPKTPVGKILRKDLR 565


Lambda     K      H
   0.319    0.135    0.412 

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: 744
Number of extensions: 37
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 556
Length of database: 566
Length adjustment: 36
Effective length of query: 520
Effective length of database: 530
Effective search space:   275600
Effective search space used:   275600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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