GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Rhodobacter viridis JA737

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_110803747.1 C8J30_RS00315 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9I6J2
         (456 letters)



>NCBI__GCF_003217355.1:WP_110803747.1
          Length = 459

 Score =  232 bits (591), Expect = 2e-65
 Identities = 143/435 (32%), Positives = 227/435 (52%), Gaps = 26/435 (5%)

Query: 20  HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAG-LWCVNVGYGREELVQAA 78
           HHL   + +K       R+  + +G+ +WD+ G + LDA +G +W VN+GYGR ++ +A 
Sbjct: 23  HHL---SQHKPYETTDPRVFVEGKGMRLWDATGREFLDATSGGVWTVNLGYGRADIARAV 79

Query: 79  TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138
             Q+  LP+Y     T   P    A+A+    P G+  V+++ SGSEAN+ V +MVR   
Sbjct: 80  QEQLLRLPYYAGAAGTV--PGARYAEALIAKMP-GLARVYYSNSGSEANEKVYKMVRQIS 136

Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQ-GDFPIPGIVHIAQPYWYGEGGD 197
                 +K  ++ R   YHG+T+A ++  G     EQ G FP  G V +     Y    D
Sbjct: 137 HRHHGGRKGKILFRERDYHGTTIAALATSGQAQRAEQYGPFP-DGFVSVPHCLEYRAQWD 195

Query: 198 MSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDI 257
           +S   +G  AA+ +E+ IL  G +++   + EPI   GGVIVPP  YW K+  I  KY+I
Sbjct: 196 VS--NYGERAADAIEEVILREGPDSIGCLVLEPITAGGGVIVPPAGYWEKVSHICRKYNI 253

Query: 258 LFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG 317
           L   DEV+CG GRTG WFG Q+YG  PD + +AKG+ SGY  +   V  + + E+     
Sbjct: 254 LLHLDEVVCGLGRTGAWFGYQHYGIQPDFVTMAKGVASGYAAISCTVTTEAVFELFKDTP 313

Query: 318 -----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELAD-HPL 371
                 F    T+ G     A ALE +RI+ +E ++E         L    ++LA+ H +
Sbjct: 314 TDPLCHFRDISTFGGCTAGPAAALETLRIIEDEGLLENT-TRMGERLLANLRDLAERHTV 372

Query: 372 VGEARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRA-------VGDTMI 424
           +G+ RG G+    ELV +++T+E   +  V  +  + C   G+++ A       +  T+ 
Sbjct: 373 IGDVRGKGLFCGAELVADRRTKEPLAEAKVQAVVAD-CAAQGVLIGATNRSIPGLNTTLC 431

Query: 425 ISPPLVIDPSQIDEL 439
           ++P L+   ++ID +
Sbjct: 432 LAPALIASEAEIDRI 446


Lambda     K      H
   0.320    0.138    0.425 

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: 574
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 456
Length of database: 459
Length adjustment: 33
Effective length of query: 423
Effective length of database: 426
Effective search space:   180198
Effective search space used:   180198
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 (21.8 bits)
S2: 51 (24.3 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