Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate WP_028488315.1 Q394_RS0105070 flavohemoprotein
Query= CharProtDB::CH_003330 (396 letters) >NCBI__GCF_000621325.1:WP_028488315.1 Length = 398 Score = 241 bits (614), Expect = 3e-68 Identities = 156/401 (38%), Positives = 221/401 (55%), Gaps = 19/401 (4%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 M+ A+++A V+AT+ L+ E G ++T+ FY MF +PELK +FNMSNQ G Q++AL +A Sbjct: 1 MITAESLAIVQATVGLVREHGTEITSTFYRSMFVTHPELKNLFNMSNQATGGQQQALASA 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFS--PGQEVLD 118 + AYA+NI N L P + +IA KH S IKP QY IVG+HLL + + E+L Sbjct: 61 VYAYAANINNPAVLEPVLSRIAHKHASLGIKPAQYTIVGKHLLGAVKTVLGDLATAEILA 120 Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGG--WEGTRDFRIVAKTPRSALITSFELEPVD 176 AW + Y +LA + REA +Y + +++ W R RIV +TP I S L D Sbjct: 121 AWDEVYWLLACDLVAREATLYAQQSARLDKQYWRTLRIERIVQETPD---IRSLYLVDPD 177 Query: 177 GGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKRE-----EGGQVSN 231 G + + GQY+ + L+ +G Q+IRQYSL+ +RI VKRE G +SN Sbjct: 178 GAKLPAFVAGQYVSIALENDGL--QQIRQYSLSDHNSQTYWRITVKREAQTECPDGFLSN 235 Query: 232 WLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVN 291 LH VGD +K P GD F+ AD+ V LISAGVG TPM+++L+TLAK + Sbjct: 236 LLH-QLTVGDTLKAGIPYGD-FVVQADNEAVALISAGVGITPMVSILNTLAKQNAALPIR 293 Query: 292 WFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGA 351 + HAA + A +V QSL + + +Y D + + G M+L ++ Sbjct: 294 FIHAARHSTQVALQTDVATAAQSLSDYRSVFFY---ETHDNVTTEDEFVGRMNLEQVALT 350 Query: 352 FSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 +YLCGP+ FM+ + L GV E IHYE FGP Sbjct: 351 DLPEKTGYYLCGPLAFMRVQREWLQAQGVPAERIHYEVFGP 391 Lambda K H 0.318 0.135 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: 373 Number of extensions: 24 Number of successful extensions: 7 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: 396 Length of database: 398 Length adjustment: 31 Effective length of query: 365 Effective length of database: 367 Effective search space: 133955 Effective search space used: 133955 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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