GapMind for catabolism of small carbon sources

 

Alignments for a candidate for QDPR in Kocuria flava HO-9041

Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate WP_058857632.1 AS188_RS03230 hemin transporter

Query= CharProtDB::CH_003330
         (396 letters)



>NCBI__GCF_001482365.1:WP_058857632.1
          Length = 400

 Score =  215 bits (548), Expect = 2e-60
 Identities = 143/402 (35%), Positives = 206/402 (51%), Gaps = 20/402 (4%)

Query: 1   MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKE-IFNMSNQRNGDQREALFN 59
           ML       VKAT+P++ E   ++   FY  MF  +PEL + +FN  NQ +G Q++AL  
Sbjct: 1   MLSDTAYPVVKATLPVVGENIQEIAKRFYAHMFAEHPELLDGLFNRGNQADGRQQQALAG 60

Query: 60  AIAAYASNIENLPALLP--AVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QE 115
           ++A YA  + N P  LP   + +IA KH S  + PEQY IV  HL+  + ++      +E
Sbjct: 61  SVAGYAGYLVNKPTELPDHLLSRIAHKHVSLGLAPEQYQIVHNHLMWAIVDVLGEAVTEE 120

Query: 116 VLDAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPV 175
           V  AW + Y ++AN  I +E  +Y   A++       R +R+V K   +A + +F +E V
Sbjct: 121 VAAAWDEVYWLMANALITQERGLYE--ATRLSPDTVWRTWRVVEKITETADVVTFVVERV 178

Query: 176 DGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEG-----GQVS 230
           D   V    PGQY+   ++     HQ  RQYSLT+  DG+    AVKR  G     G++S
Sbjct: 179 DEREVKPSLPGQYVTCKMEMPDGVHQP-RQYSLTKADDGRHRVFAVKRIRGNGTPAGEMS 237

Query: 231 NWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQV 290
             LH+   +GD + L AP GD  +   D  PV L+SAG+G TPM  ML  L   G   +V
Sbjct: 238 TLLHDQVQIGDEITLSAPFGDVVLEYTD-RPVVLVSAGIGITPMAGMLSHLVAGGAQRKV 296

Query: 291 NWFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEG 350
              HA  + +  A   +V    + L   +   W+  PS A    G  +  GLMD+  +E 
Sbjct: 297 LLLHADASPESFALRAQVTADLEELLDGSLAVWFEHPSPAP---GPNEHAGLMDVRAVE- 352

Query: 351 AFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392
                  Q+YLCGP+ FMQ     L+  GV  ++I YE FGP
Sbjct: 353 --LPAQAQYYLCGPLPFMQAVRSDLIARGVPAKDIQYEVFGP 392


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: 439
Number of extensions: 24
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: 396
Length of database: 400
Length adjustment: 31
Effective length of query: 365
Effective length of database: 369
Effective search space:   134685
Effective search space used:   134685
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.

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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