GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc02120
          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:

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