GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Sinorhizobium meliloti 1021

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate SMc03118 SMc03118 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Smeli:SMc03118
          Length = 295

 Score =  141 bits (355), Expect = 2e-38
 Identities = 91/296 (30%), Positives = 157/296 (53%), Gaps = 13/296 (4%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           ++ F+ QLL GL  GS Y L+++G  +++G++ +INFAHG  +MLG F A   +L+L+ +
Sbjct: 9   LQAFLGQLLIGLINGSFYALLSLGLAIIFGLLRVINFAHGAQYMLGAFMA---WLLLSYL 65

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
             G   A      L++A L+  L    IER   R L     L  L+   G+++T+    +
Sbjct: 66  GIGYWPA------LILAPLLVGLIGAVIERTMLRRLYTLDPLYGLLFTFGLALTIEGTFR 119

Query: 121 VTQGPRNKP--IPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178
              G   +P   P ++      G + + + +  +IV + V+    W ++ +T LG   RA
Sbjct: 120 YLYGASGQPYATPALLMGGANLGFMFLPIYRGWVIVFSLVICLGTWLMIEKTKLGSYLRA 179

Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238
             ++  +    G+NV   +++T+ +GAALAA+AG +    Y V+    G    +  F   
Sbjct: 180 ATENPVLVQSFGINVPFLLTLTYGLGAALAAIAGVLAAPIYQVSPLM-GSNIIIVVFAVV 238

Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294
           V+GG+GS+ GA+  G L+G+ E L   ++  A  ++  F I+A VL+ +P G+ GR
Sbjct: 239 VVGGMGSIMGAIVTGYLLGIAEGLTKVFYPEA-SNIVIFVIMAIVLLLRPAGLFGR 293


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: 294
Number of extensions: 20
Number of successful extensions: 5
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: 295
Length adjustment: 26
Effective length of query: 274
Effective length of database: 269
Effective search space:    73706
Effective search space used:    73706
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 17 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