GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Desulfatibacillum aliphaticivorans DSM 15576

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_028316922.1 G491_RS0128270 pyridoxal-phosphate dependent enzyme

Query= BRENDA::Q96GA7
         (329 letters)



>NCBI__GCF_000429905.1:WP_028316922.1
          Length = 309

 Score =  274 bits (700), Expect = 2e-78
 Identities = 150/315 (47%), Positives = 197/315 (62%), Gaps = 9/315 (2%)

Query: 13  PFHVVTPLLESWALSQVAGMPVFLKCENVQPSGSFKIRGIGHFCQEMAKKGCRHLVCSSG 72
           P H+ TPLLE   L +  G  + LK E +QP GSFKIRG+G+ CQ+  ++G  HL+ SS 
Sbjct: 3   PIHIHTPLLEHRLLGEAIGRKILLKMECLQPPGSFKIRGVGYLCQKAVERGVTHLISSSA 62

Query: 73  GNAGIAAAYAARKLGIPATIVLPESTSLQVVQRLQGEGAEVQLTGKVWDEANLRAQELAK 132
           GNAG A AYA RKLG+  T+V PES+S +  + +Q E AE+ + G+ WD+A++RAQE   
Sbjct: 63  GNAGYATAYAGRKLGVKVTVVAPESSSPRARELIQSEKAELIIHGQAWDDAHVRAQECLL 122

Query: 133 RDGWENVPPFDHPLIWKGHASLVQELKAVLRTPPGALVLAVGGGGLLAGVVAGLLEVGWQ 192
            +    VPPFDHP +W GH+SLV EL A     P A+VL+VGGGGLL GV+ G+   GW+
Sbjct: 123 DEKCAYVPPFDHPDLWTGHSSLVDEL-AEQCGKPDAVVLSVGGGGLLCGVLEGMERHGWK 181

Query: 193 HVPIIAMETHGAHCFNAAITAGKLVTLPDITSVAKSLGAKTVAARALECMQVCKIHSEVV 252
            VP+IA ET GA  F  ++  G LV L  ITS+A+SLGAKT +  AL+     ++   VV
Sbjct: 182 DVPVIAAETRGADSFAQSVAQGSLVHLDAITSIAQSLGAKTASQAALDWTFRHEVRPAVV 241

Query: 253 EDTEAVSAVQQLLDDERMLVEPACGAALAAIYSGLLRRLQAEGCLPPSLTSVVVIVCGGN 312
            D +AV A     +D ++LVEPACGA+LAA Y   LR LQ          +VVVIVCGG 
Sbjct: 242 SDKDAVKACLAFAEDRKVLVEPACGASLAAAYDN-LRELQ-------DAKTVVVIVCGGI 293

Query: 313 NINSRELQALKTHLG 327
            +    + A K   G
Sbjct: 294 GVTLNRMWAWKKEFG 308


Lambda     K      H
   0.319    0.134    0.404 

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: 254
Number of extensions: 11
Number of successful extensions: 2
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: 329
Length of database: 309
Length adjustment: 28
Effective length of query: 301
Effective length of database: 281
Effective search space:    84581
Effective search space used:    84581
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: 48 (23.1 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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