GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Nocardioides daejeonensis MJ31

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_110206119.1 DNK54_RS06380 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_003194585.1:WP_110206119.1
          Length = 299

 Score =  140 bits (354), Expect = 3e-38
 Identities = 99/314 (31%), Positives = 157/314 (50%), Gaps = 29/314 (9%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M  F +  + GL LG+IY L+A+G+ MVY   G++NFA G+   LG F        L + 
Sbjct: 1   MTQFAELTIAGLALGAIYSLIAVGFVMVYRSSGLLNFAQGEFATLGAF--------LMTT 52

Query: 61  FAGL-----PVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITL 115
           FA       PVA+LL V++++A+ M       IERV  R L G       I  I +   L
Sbjct: 53  FAAWAVLPWPVALLLTVLVMMAVGMG------IERVIMRKLLGRPPFIGSIVTIFVGFLL 106

Query: 116 SNFIQVTQGP--RNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALG 173
           S  +    G   R  P P     + + G +  +L  ++ I++  VL+    +++ RT +G
Sbjct: 107 SVAVLWIYGSSTRAMPTPWDPVKIVEVGGVEFTLTNLVTILVAIVLIGTLAFVMQRTPMG 166

Query: 174 RAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVK 233
            A RA   D++ A  LG+ V++ + +T+ + A+L AVAG    M+   A+   G     +
Sbjct: 167 MAMRAVADDQEAAFALGIPVERLLGLTWGIAASLGAVAGVFLAMFPRSATVAMGLL-AFR 225

Query: 234 AFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAY-------FTIAYKDVATFAILAFVLIF 286
           AF A ++GG+ S  GA+ GG  +GL++     Y       F I +  V  F ++   L+ 
Sbjct: 226 AFPAVIIGGLESPVGAIIGGSALGLLQVHGEYYVNPHLGDFGIGFHLVLAFIVMIAFLMI 285

Query: 287 KPTGILGRPEVEKV 300
           KP G+ G  E+E+V
Sbjct: 286 KPHGLFGTKELERV 299


Lambda     K      H
   0.329    0.143    0.421 

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: 287
Number of extensions: 18
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: 300
Length of database: 299
Length adjustment: 27
Effective length of query: 273
Effective length of database: 272
Effective search space:    74256
Effective search space used:    74256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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