Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_050463100.1 AKL27_RS12205 C-terminal binding protein
Query= BRENDA::Q61753 (533 letters) >NCBI__GCF_001189915.1:WP_050463100.1 Length = 319 Score = 138 bits (348), Expect = 3e-37 Identities = 96/304 (31%), Positives = 158/304 (51%), Gaps = 9/304 (2%) Query: 8 KVLISDSLDPCCR---KILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVI 64 KVLI+D P + ++ G++VV Q ++EE+IA C+GL+V+ A V A V Sbjct: 2 KVLITDYDFPDVELELALYREAGIEVVTAQCHTEEEVIAAAAGCQGLLVQYAP-VNAKVF 60 Query: 65 NAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQA 124 A ++++ R G G D ++ A + G+ V N+P+ + M + L R I Sbjct: 61 AARPEIRIASRYGAGFDTINTADAAKYGVWVGNSPDYGVGEVSTHALAMALDLIRNITAY 120 Query: 125 TASMKDGKWDRKKFMGTELNGK-TLGILGLGRIGREVATRMQSFGMKTVGYDP-IISPEV 182 +K G+W + + T+GI+GLGRIG+ +A ++ + + YDP II + Sbjct: 121 DRDVKAGQWHYTTAGKIQRASEMTIGIVGLGRIGKRMAHISRNLFKRVIAYDPHIIDGDF 180 Query: 183 AASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDSTFAQCKKGVRVVNCARGGIVDE 242 A V+++ EE++ D +++HTPL T G++N S + +VN ARGG+V+ Sbjct: 181 PAY--VERVSKEELFRQADLVSLHTPLNDETRGMINASVLNLMQPESFLVNSARGGLVNI 238 Query: 243 GALLRALQSGQCAGAALDVFTEEPPR-DRALVDHENVISCPHLGASTKEAQSRCGEEIAV 301 LL+AL S + GA LDV EPP+ A+V H+ V+ PH ++ A + + A Sbjct: 239 DDLLQALDSNRLKGAGLDVLPVEPPQTSSAIVQHKRVLLSPHAAFYSEVAAAELRRKAAQ 298 Query: 302 QFVD 305 +D Sbjct: 299 NLID 302 Lambda K H 0.318 0.134 0.395 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: 337 Number of extensions: 15 Number of successful extensions: 4 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: 533 Length of database: 319 Length adjustment: 31 Effective length of query: 502 Effective length of database: 288 Effective search space: 144576 Effective search space used: 144576 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
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