GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Lacinutrix algicola AKS293

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19 (characterized, see rationale)
to candidate WP_055435130.1 ASC41_RS02805 3-phosphoshikimate 1-carboxyvinyltransferase

Query= uniprot:I9A2E3
         (408 letters)



>NCBI__GCF_001418085.1:WP_055435130.1
          Length = 411

 Score =  309 bits (792), Expect = 9e-89
 Identities = 183/406 (45%), Positives = 259/406 (63%), Gaps = 19/406 (4%)

Query: 13  TTIQLPSSKSISNRALIINALGNRTFQLENLSDCDDTQVMIHALNDGKNTIDIMAAGTAM 72
           + IQ+  SKS SNR L++ AL      +EN+S+ DD+Q+M  AL   +  IDI  AGTAM
Sbjct: 14  SAIQITGSKSESNRLLLLQALYPE-INIENVSNSDDSQLMTKALAATEQVIDIHHAGTAM 72

Query: 73  RFLTAYLSVTPGTR-IITGTQRMQQRPIQVLVNALRELGAEIEYIINDGYPPLRITGHKL 131
           RFLTAY +       IITG++RM++RPI++LV+AL +LGA+I Y  N+GYPPL I G +L
Sbjct: 73  RFLTAYFATQNNRETIITGSKRMKERPIKILVDALNQLGADISYKENEGYPPLLIKGKQL 132

Query: 132 QKDTISLPGNVSSQYISALLMIAPILSNGLTLTLTGEIISRPYINLTLQLMNDFGARAKW 191
            K+ +SL  NVSSQYISALL+IA  L NGL LTL G+I S PYIN+TL L+++     K+
Sbjct: 133 TKNKVSLDANVSSQYISALLLIASKLENGLELTLNGKITSVPYINMTLSLLSELNIETKF 192

Query: 192 ------LNEYQLKVEPQPYQSIPFYVESDWSAASYWYQIAALSN-KAEIILPGLFETSYQ 244
                 +   Q K+EP+        VESDWS+ASY+Y I AL+     I +    + S Q
Sbjct: 193 EGNVITVKPLQKKLEPK-----TLTVESDWSSASYFYSIVALAEVGTSIEISSYKKDSLQ 247

Query: 245 GDSKVAEIFQLLGIESIYGNKTVTLKKTDKITER--LDYDFINQPDLAQTFVVTCALMNI 302
           GDS +AEI++  G+ +++ +K V L K +++ +   +D++  N PD+AQT  VT   + +
Sbjct: 248 GDSALAEIYKSFGVSTVFQDKGVLLTKENEVNKETAIDFNLANSPDIAQTIAVTAFALGL 307

Query: 303 PFRFSGLQSLKIKETDRMAALIQEMGKLGYILHETDDRILSWEGERCEMTADVAIDTYED 362
               +GL +LKIKETDR+ AL  E+ KLG  +  T++ +      +  +  +VAI TY D
Sbjct: 308 ESNLTGLHTLKIKETDRLEALKTEIEKLGGAVDITNETLHLKVTNK--IKENVAIATYND 365

Query: 363 HRMAMAFAPACVVMPEIRINNPQVVSKSYPYYWEDLKKAGFIIEEV 408
           HRMAMAFAP  +  P + I +  VVSKSYP +W+DLK+ GF I+ +
Sbjct: 366 HRMAMAFAPLALKTP-LEIEDYMVVSKSYPTFWDDLKQLGFDIKAI 410


Lambda     K      H
   0.320    0.135    0.391 

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: 379
Number of extensions: 15
Number of successful extensions: 9
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: 408
Length of database: 411
Length adjustment: 31
Effective length of query: 377
Effective length of database: 380
Effective search space:   143260
Effective search space used:   143260
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: 50 (23.9 bits)

This GapMind analysis is from Jul 26 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