GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Lutibaculum baratangense AMV1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_023434295.1 N177_RS20200 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:Q1MCU1
         (463 letters)



>NCBI__GCF_000496075.1:WP_023434295.1
          Length = 441

 Score =  430 bits (1105), Expect = e-125
 Identities = 238/458 (51%), Positives = 302/458 (65%), Gaps = 29/458 (6%)

Query: 10  KPDAGLVRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIG 69
           +P A LV+    +A ++A+++  +    +GL+T       L +  RW  + + V     G
Sbjct: 9   RPAAELVK----DAAYSALIALALAAPIIGLQT-VTARGGLGLNARWDDVFLIVLAVFAG 63

Query: 70  RFAMVVFIRPNIDRRKLSKA---REGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIK 126
           R  +   I  +   R + +    R G    +       +    +AL   LL P +  + +
Sbjct: 64  RLLLNFTIWRHQGARPIGQKWFQRAGGRPFARHGHTLSKIIGPLALAVALLLPALPFSDR 123

Query: 127 GPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGL 186
                  YV +  I +L Y+ML WGLNIVVGLAGLLDLGYVAFYA+GAYS+ALL+++F L
Sbjct: 124 -------YVMDLSIMVLTYIMLGWGLNIVVGLAGLLDLGYVAFYAIGAYSFALLATHFDL 176

Query: 187 SFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGI 246
            FW+ LPL+GI AA WGVILGFPVLRLRGDYLAIVTLAFGEIIR+VL+NW + T G  GI
Sbjct: 177 GFWICLPLAGILAAFWGVILGFPVLRLRGDYLAIVTLAFGEIIRVVLLNWYEFTGGPNGI 236

Query: 247 SSIPKATLFGIPFDATAGG-FAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMP 305
             IP  TLFG+ F       F + F L  SS +  IFL+Y+IL L ++T +VT+RLRR+P
Sbjct: 237 LGIPDPTLFGLEFARRGDNTFHEFFGLSYSSMHKIIFLYYIILCLALITNFVTLRLRRLP 296

Query: 306 IGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLE 365
           +GRAWEALREDEIACRSLGINT  TKLTAFA GAMF GFAGSFFA RQGF+SPESF F+E
Sbjct: 297 VGRAWEALREDEIACRSLGINTTNTKLTAFAIGAMFGGFAGSFFATRQGFISPESFTFIE 356

Query: 366 SAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLA 425
           SA+ILAIVVLGG+GS  G+ IAAIVM+GG E  RE              E YRMLIFGLA
Sbjct: 357 SALILAIVVLGGLGSQVGVVIAAIVMMGGFEYFREF-------------EQYRMLIFGLA 403

Query: 426 MVVVMLFKPRGFVGSREPTAFLRERKAISGSFIKEGHG 463
           MV +M+++PRG + +R P+  L+ERKAI    + +GHG
Sbjct: 404 MVFIMVWRPRGLISTRSPSVILKERKAIGADLVGQGHG 441


Lambda     K      H
   0.330    0.145    0.432 

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: 673
Number of extensions: 36
Number of successful extensions: 3
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: 463
Length of database: 441
Length adjustment: 33
Effective length of query: 430
Effective length of database: 408
Effective search space:   175440
Effective search space used:   175440
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: 51 (24.3 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