GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5404 in Sinorhizobium meliloti 1021

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate SMc02120 SMc02120 general L-amino acid transport permease ABC transporter protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>lcl|FitnessBrowser__Smeli:SMc02120 SMc02120 general L-amino acid
           transport permease ABC transporter protein
          Length = 384

 Score =  400 bits (1027), Expect = e-116
 Identities = 204/367 (55%), Positives = 251/367 (68%), Gaps = 13/367 (3%)

Query: 11  PPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRADCT 70
           P P    G V+W+R N+F++  +T LT+ +  ++  +VPP +QW  +DA W G  R  C 
Sbjct: 18  PAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAAWSGGGRGVCA 77

Query: 71  K-----------EGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFP 119
                        GACW F+  +F QF++G YP D RWR  L   L V+ + P+ I R P
Sbjct: 78  TLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALVGILFVLLLVPMLIPRIP 137

Query: 120 RKAIYGLSFLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVL 179
            K +  L  LV  PI +  LL GG FGL  V T  WGGLM+TLV++ VGI  +LPLGI+L
Sbjct: 138 YKGLNALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILL 197

Query: 180 ALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVIL 239
           ALGRRSNMP I+++C  FIE  RGVPLITVLFM+SVMLPLFLP+G+ FDK LRALIGV L
Sbjct: 198 ALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKFLRALIGVSL 257

Query: 240 FQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALF 299
           F SAY+AEVVRGGLQAIPKGQYE A ++GL +W+ MG ++LPQALKLVIPGIVNTFI LF
Sbjct: 258 FASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLF 317

Query: 300 KDTSLVIIIGLFDLLNSVKQAAADPKWLGMAT--EGYVFAALVFWIFCFGMSRYSMHLER 357
           KDTSLV IIG+FDLL  V+   +D  W    T   G +FA  VFW+FCFGMSRYS  +ER
Sbjct: 318 KDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMER 377

Query: 358 KLDTGHK 364
            LD   +
Sbjct: 378 LLDRSQR 384


Lambda     K      H
   0.330    0.144    0.469 

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: 631
Number of extensions: 28
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: 365
Length of database: 384
Length adjustment: 30
Effective length of query: 335
Effective length of database: 354
Effective search space:   118590
Effective search space used:   118590
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 (21.9 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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